From: LTR retroelements are intrinsic components of transcriptional networks in frogs
Domain | Pfam No. | Included in | Domain description/function | Ref. |
---|---|---|---|---|
CHROMO (Chromatin organization modifier) | pfam00385 | This domain was exclusively found within Amn-san elements. Circa 80% of these elements within the Silurana genome encode for a chromo domain. | The chromo domain is about 40–50 amino acids long. It is contained in various proteins involved in chromatin remodeling and the regulation of gene expression in eukaryotes during development. | |
PNMA (Para-neoplastic antigen MA) | pfam14893 | Found so far in about 30% of Cer elements and in about 16% of Gmr elements. | This protein domain has so far only been studied in mammals, where it has been associated with neurological disorders. | |
Because of the homology between PNMA proteins and an apoptosis inducing protein (MOAP1), the involvement of PNMA proteins in apoptosis is hypothesized. | ||||
SCAN | pfam02023 pfam00096 | This domain was found in over 50% of Gmr elements only. | The SCAN domain family of Zinc finger transcription factors, they are thought to be implicated in regulating genes involved in lipid metabolism, cell survival, and differentiation. | [61] |
Exo/endo phosphatase | pfam03372 pfam14529 | Found in about 12% of Mtanga elements. | The exo-/endonuclease phosphatase family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signaling. | |
Zinc Fingers Zf-H2C2_2 (Zinc-finger double domain) Zf-CCHC (Zinc knuckle) | pfam13465 | About 40% of SnRVs contained a Zinc-finger double domain; about 20% of XEN1 elements contained a Zinc knuckle. | Zinc finger (Znf) domains are relatively small but very diverse protein motifs which can target specific molecules. Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organization, epithelial development, cell adhesion, protein folding, chromatin remodeling, and Zinc sensing, to name but a few. | |
pfam00098 | A Zinc knuckle is a Zinc binding motif of the general structure CX2CX4HX4C where X can be any amino acid. The motifs mostly originate from retroviral gag proteins (nucleocapsid). Zinc knuckles are involved in eukaryotic gene regulation. | |||
UBN2 gag-polypeptide of LTR copia-type | pfam14223 | Found in Copia-type elements, in about 30% of Mtanga elements and in about 80% of Hydra1.1 elements. | Ubinucleins are members of a protein family that contain a conserved HIRA binding domain which interacts with the N-terminal WD repeats of HIRA/Hir proteins. UBN1 and UBN2 are believed to be the orthologs of Hpc2p, a subunit of a nucleosome assembly complex in budding yeast (HIR), involved in regulation of histone gene transcription. | [66] |