The Chromodomain Type 1 Integrase-like (CIN-1) is the name we give to the pool of transposases typically encoded by the the self-synthesizing Maverick/Polinton transposons of eukaryotes (Feschotte & Pritham 2005; Pritham et al. 2007; Kapitonov & Jurka 2006). CIN1 TRs present an integrase-like core with no N-terminal HHCC module and a C-terminal chromodomain (Koonin et al. 1995; Wright et al. 2005; Singleton & Levin 2002), similar to that found in the integrases (INTs) coded by Ty3/Gypsy chromoviruses and a particular clade of Ty1/Copia elements called CoDi-I (Maumus et al. 2009; Llorens et al. 2009). The chromodomain (the chromatin organization modifier) is a small protein module involved in chromatin re-modeling, regulation of gene expression (Koonin et al. 1995), and differential host genome integration of LTR retroelements Wright et al. 2005; Singleton & Levin 2002).

CIN-1 TRs where originally described (together with SCAN/KRAB INTs), as members of a large pool of INTs related to FOB1 and LTR retroelement INTs (Gao & Voytas 2005). Because of the assumption of a cellular role for these enzymes, they were called cellular integrases (C-INTs). The accepted notion in the origin of these enzymes was that they evolve from LTR retroelement INTs but such hypothesis underwent an exciting turn with the discovery that CIN-1 TRs are not host genes but TR components of Maverick/Polinton transposons. Evaluation of insect genomes such as that of the Pea Aphid Acyrthosiphon pisum (The International Aphid Genomics Consortium 2010) however suggests that CIN-1 TRs can also be found as Solo-TR encoding transposons organized as both intron-exon structured genes and as single ORFs without introns of 0.8-2.4 kb (Llorens et al. manuscript in preparation). For simplicity´s sake the figure below shows the genomic structure without introns.


There are three complementary classifications for CIN-1 TRs. Based on sequence these enzymes can be classified as DDE TRs and INTs. Based on INT-like structural potential similarities, CIN-1 TRs are members of the Retroviral Integrase Superfamily (Nowotny 2009) of nucleic acid-processing enzymes involved in; a) selfish evolution; b) replication and repair of DNA; c) recombination and gene fusion; d) RNA-mediated gene silencing; and e) oncogenesis. Based on their usual mobile genetic element carrier these enzymes can be classified as Maverick/Polinton transposons (Feschotte & Pritham 2005; Pritham et al. 2007; Kapitonov & Jurka 2006).

Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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