Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains

Abstract

Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.

Keywords: Genetic surveillance; Genome complexity; TREome gene profile; TREome landscape; Transposable repetitive elements (TREome).

Fig. 1

High-level diversity in MLV-ERV (TREome) LTR sequences among 12 laboratory mouse strains. The extent of variations among the population of MLV-ERV LTR sequences from the genomic DNA of 12 mouse strains were examined by a probability distribution function analysis for 4-nucleotide word sets. The extent of variations for the individual words were visualized on a 16 × 16 (= 256) matrix. In contrast to the overall low variation matrix of GAPDH genes (a conventional gene) from 20 laboratory mouse strains (right panel), the vast majority of the words from the MLV-ERV sequences derived from 12 mouse strains (left panel) had a high-level of variability. Variability of each word within individual sets (12 [MLV-ERV LTR] strains or 20 [GAPDH gene] strains) is coded on a gray scale, ranging from white (low = 0) to black (high = 0.001261).

Fig. 2

Polymorphic TREome landscapes among the genomes of 56 laboratory mouse strains. Using MLV-ERVs as a probe, TREome landscapes of the genomes of 56 laboratory mouse strains were visualized. None of the 56 mouse strains share the same TREome landscape patterns. Distinct TREome landscape patterns were found within certain families of strains (highlighted with dotted lines and colors), such as 129PI-XI/, A/, BALB/, C3H/, C57BL/, DBA/, and MOL. The TREome landscapes of the C3H/HeJ and C3H/HeOuJ strains were different (one of the different bands is indicated with an arrow). In addition, three strains (Mus caroli/Ei, Mus Pahari/Ei, and PANCEVO/Ei) had only a couple of visible bands. SM (size marker).

Fig. 3

Un-identical TREome landscapes between the C3H/HeJ strain and its wildtype control, C3H/HeOuJ. With respect to the TREome landscape patterns, the C3H/HeJ strain (TLR4^−/−) is markedly different from its presumed wildtype control, C3H/HeOuJ (TLR4^+/+), in the genomes of all six organs (kidney [KI], liver [LI], lung [LU], lymph node [LN], spleen [SP], and thymus [TH]) examined. In particular, one distinct TREome band (enlarged in a separate window) was found only in the C3H/HeJ strain while another band was present only in the C3H/HeOuJ strain. SM (size marker).

Fig. 4

Apparent variations in TREome landscapes between the CD14 knock-out strain and its backcross-control, C57BL/6J strain. There were apparent differences in the TREome landscapes between the genomes of CD14 knock-out and its backcross-control (C57BL/6J) strains in all six organs (kidney [KI], liver [LI], lung [LU], lymph node [LN], spleen [SP], and thymus [TH]) examined. Two unique TREome bands were visible only in the CD14 knock-out strain, whereas two other bands were found only in the C57BL/6J control strain. SM (size marker).

Fig. 5

TREome landscapes of 129 mouse substrains. Genomic DNAs of nine 129 substrains (129S1/SvImJ [A], 129/Sv-Lyn^tm1Sor/J [B], 129S1/Sv-Oca2⁺ Tyr⁺ Kitl^Sl-J/J [C], 129S4/SvJae-Inhbb^tm1Jae/J [D], 129S4/SvJae-Ppara^tm1Gonz/J [E], 129S4/SvJaeSor-Gt(ROSA)26Sor^tm1(FLP1)Dym/J [F], 129S6/SvEv-Mos^tm1Ev/J [G], 129P1/ReJ [H], and 129X1/SvJ [I]) were examined for variations in TREome landscapes. Overall, all substrains shared a similar TREome landscape pattern; however, both of the 129/Sv-Lyn^tm1Sor/J and the 129P1/ReJ substrains lacked a unique band in its TREome landscape compared to the other seven strains. SM (size marker).

Fig. 6

TREome landscape-based monitoring of genome-crossing between two mouse strains: an example. We examined whether the genome-crossing events between two mouse strains (C57BL/6J x 129S1/SvImJ) are reflected in the TREome landscapes of a hybrid offspring. For the most part, the pattern of the F2 hybrid's TREome landscape included the bands from both the C57BL/6J and 129S1/SvImJ genomes; however, certain bands specific for the individual parental strains were not present. This F2 hybrid's TREome banding pattern provides valuable information which visualizes the genomic status of crossing events between two strains. SM (size marker).

Fig. 7

Highly polymorphic TREome gene (MMTV-ERV SAg) isoforms among 46 laboratory mouse strains. Polymorphisms in the MMTV-ERV SAg gene coding regions among 46 laboratory mouse strains were examined. A. A high-level of MMTV-ERV SAg gene polymorphism was apparent among the genomes of the 46 mouse strains; altogether, 183 MMTV-ERV SAg gene isoforms were identified. In addition, the C-terminus regions of the MMTV-ERV SAg gene coding sequences had relatively high levels of variations compared to the other regions. B. MMTV-ERV SAg isoform profiles were different between the C3H/HeJ inbred strain (eight unique isoforms) and its wildtype TLR4 control strain, C3H/HeOuJ (five unique isoforms).