What is the difference between intergenic and intragenic

Sorek, R. Prokaryotic transcriptomics: A new view on regulation, physiology and pathogenicity. Nature Reviews Genetics, 11 , 9. Tokajian, S. Frontiers in Microbiology, 7 , 1—8. Ulitsky, I. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell, 7 , — Venter, J.

The sequence of the human genome. Science, , — Wolstenholme, D. Animal mitochondrial DNA: Structure and evolution. International Review of Cytology, , — Yamada, M. Functions of long intergenic non-coding linc RNAs in plants. Journal of Plant Research, , 67— Akash Gautam 1 1. However, no length dependence of the recombination frequency in intergenic crosses with a distance between mutations of to greater than bp is observed.

We attribute this lack of dependence to the high rate of viral DNA interchange, which makes some step other than the cross-over event rate-limiting. Furthermore, we believe that the observed difference in recombination frequency between inter- and intragenic recombination is due to complementation between temperature-sensitive mutants at the permissive temperature.

These putative L1 sequences were compared with the full-length L1s, i. The intactness conservation from each of these characteristics was calculated by comparing it with the corresponding locus on the reference L1s. These characteristics can be used to predict the status of L1 activity [9] , [21].

From that definition, conserved means conservation of protein functional motifs and RNA structural elements that altogether are necessary and sufficient for retrotransposition [9].

These functional motifs include ORF boundaries, promoter motifs, poly A terminator, and important amino acid residues [9] , [21]. Such subfamily information are thought to reflect L1 age by using the assumption that sequence divergence increases with age [23] , [24]. Two statistical tests, namely chi-square test for categorical characteristics and Student's t -test for non-categorical characteristics, were conducted to test the null hypothesis that for a given feature of L1, there should not be much different between intragenic and intergenic L1s.

Statistical tests were conducted separately on both mouse and human L1s. In mouse, there are 42 categorical functional characteristics and 11 non-categorical characteristics of L1s Table S1. In human, there are 33 categorical and 18 non-categorical characteristics of L1s Table S2. MH chi-square operates by combining the chi-square tests performed separately on each L1 stratum grouped by the aforementioned L1 subfamilies. MH p-values and MH odds ratios OR between L1s located in the intragenic and intergenic region were then calculated for each feature.

An OR greater than one indicates that the L1 status tested conserved, etc. For non-categorical quantitative features, unpaired Student's t -tests with unequal variances [26] were performed between intragenic and intergenic L1s.

The quantitative features tested for mouse L1s include GC content and intactness score, i. To test the hypothesis that intragenic L1s regulate genes in other physiological cellular processes such as embryogenesis in mammalian species, we analyzed publicly available microarray data from different stages of preimplantation embryonic development, namely one-cell, two-cell, four-cell, eight-cell, sixteen-cell, morula and blastocyst stages GEO accession number GSE [27].

The gene regulation profiles of one-cell stage were compared with all other stages for human and mouse. Differentially expressed genes between each developmental stage and the one-cell stage were identified using paired Student's t -test [28]. Paired t -statistics were calculated from the average and standard deviation of differences between paired samples of each developmental stage and the one-cell stage.

Genes with p-values less than 0. Chi-square analysis was then performed to test if genes containing L1 sequences are associated with up regulation with respect to the one-cell stage. First, we determine densities of the intragenic L1 group and intergenic L1 Figure 1A on autosome, X and Y chromosomes.

Except for the Y chromosome, L1 density is much greater in mouse than that of human Figure 1B. Intragenic L1 density is lower than intergenic for autosomes and X chromosome of both species, whereas the density of intragenic L1s is greater in the Y chromosome of both species Figure 1C.

The denseness of intragenic L1s in Y-chromosome Chr. Y cannot be explained by the compactness of Chr. The percentage of intergenic region is always larger than intragenic region on all chromosomes and is largest for the Y chromosome. In the human genome on average, Intergenic contents in mouse are similar Previous study showed that intragenic human L1s are more conserved than intergenic ones [17].

Conversely, sporadic frameshifts, gaps, and stop codons are more common in intergenic L1s. The greater conservation of human intragenic L1 sequences may reflect functions dependent on L1 transcription [17].

The conservation and distinction of intragenic and intergenic L1 sequences in mouse and human were tested by Mantel-Haenszel chi-square and unequal variance Student's t -tests Figure 2 and 3. The Mantel-Haenszel p-value measurement was presented in —log 10 p-value , where the higher number represents more significant value. From these tests, it was found that intragenic L1s are significantly more conserved in mouse as well as human. Only one functional feature, the SA acceptor splice site on antisense mouse L1 sequences, is poorly conserved among intragenic mouse L1.

For both mouse and human, intragenic L1s have significantly higher intactness score and GC contents than that of intergenic L1s. For human L1s, ORF1 and ORF2 codon adaptation indexes CAI are significantly higher for intragenic L1s, whereas for mouse intragenic L1s, the monomer features, namely mean number of monomer repeats and monomer splice sites, are significantly greater.

The complete listing of functional features and their statistical values are in Table S1 and S2 , respectively. Our analyses indicate that many important features of mouse L1 sequences are well conserved in intragenic L1s. Therefore, like human intragenic L1s, the conservation of structural features could suggest a similar transcriptional role. The structure of mouse L1 is shown under the bar graph to indicate the relative location of the feature in L1 sequence.

The blue columns indicate that more of these features appear in the intragenic L1s than that of intergenic ones. The red columns indicate that there are more of such features in the intergenic L1s than that of intragenic ones. A A bar graph shows 15 significant features passing the significance p-value 1. The green and orange bars represent conserved and mutated features, respectively. These colored bars are aligned with L1 structure shown below the graphs.

B A bar graph shows non-categorical features whose significance p-value pass 1. L1s are expressed in early embryogenesis [16] , and L1 products are essential for development [30]. It is not known, however, if expression of intragenic L1 regulates expression of gene pre-mRNA in embryogenesis similar to what was reported in cancer [17]. We analyzed microarray expression data of mouse and human early embryonic stages and tested whether changes in expression are associated with intragenic L1s.

In mouse, the observed numbers of genes with intragenic L1 and down-regulated relative to the one-cell stage are significantly higher than expected for all stages except blastocyst. In contrast, no significant association was found for up-regulated genes and intragenic L1s Table 1. Significantly higher than expected numbers of down-regulated genes with intragenic L1s were also found for human embryonic stages, albeit only the latter three stages, i.

Among the stages with significant association of intragenic L1 and down-regulation, genes are commonly down regulated among mouse stages whereas are common among human stages Figure 4. Among the genes in these two intersection sets, 14 are orthologous between mouse and human, according to the mouse genome database [31]. Using Gene Ontology [32] and GeneCards [33] , the molecular functions of these orthologous genes are listed in Table S3. A Intersection of 4 gene sets in mouse genome.

Each gene set is represented by a colored oval. B Intersection of 3 gene sets in human genome. A colored circle represents each gene set. C Name listing of mouse-human orthologous genes found in both mouse and human intersection gene sets. Each orthologous gene pair indicates the mouse gene name followed by the human gene name.

The numbers in parentheses present the corresponding gene ids. In this study, we tested for association of L1 location and sequence with respect to genes and L1 functions in two mammal species. Four main observations were made. First, L1 density is greater in mouse than human, including L1s within genes.

Second, intergenic L1s density is greater in autosome and X-chromosome but less in Y-chromosome. Third, mouse intragenic L1s are less conserved than human and contain significantly more monomer repeats than that of intergenic ones. Finally, mouse and human intragenic L1s are associated with down-regulation of gene expression during early embryogenesis. On the X-chromosome, L1 density is higher than all other chromosomes combined in mouse and human.

This is consistent with the role of L1s in X-inactivation activity, where L1s are thought to act as boosters of X-inactivation chromosome spreading from a center of inactivation [12] , [13]. For autosomal and X-chromosomes, intergenic L1 densities are much higher than intragenic ones. The lower density of intragenic versus intergenic L1 in both species suggests that L1 retrotransposition into genes is likely to be deleterious and would selected against in evolution [34].

This purifying selection in the X and autosomes could be facilitated by recombination of homologous chromosomes or homologous recombination DNA break repair. Y-chromosome is hemizygote and majority of the chromosome lacks homologous recombination. If the role of intergenic L1s is related to homologous recombination or homologous chromosome, intergenic L1s in Y-chromosome may have no function and can be considered as junk DNA.

Rearrangements and deletion mutations of intergenic L1s in Y-chromosome should not affect fitness and the L1s should be continuously lost during evolution. In contrast to intergenic L1s, intragenic L1s possess gene regulatory function and should be conserved [14] , [16] , [17]. As a result, in Y-chromosome, intragenic L1 density is higher than intergenic for both mouse and human.