Genome is the blueprintwhich contains all the relevant and irrelevant information which is requiredfor the human being for its growth and development.
Earlier until the discoveryof jumping genes, relevant information in the genes was expressed in proteinsand carry out specific biological function. The perspective of genome changedslowly after the revolutionary and ground-breaking discovery by BarbaraMcClintock of mobile elements (Goodier et al, 2016). This discovery witnessedthe fluidity and dynamics of the genome which was supposed to be carried out bythe mobile genetic elements. They might play a great role in the evolution ofthe genes and how their shape and function change with time. Mostly genome contains repetitivesequences and transposable genetic elements comprise of more than 45% of thehuman genome. Transposable elements can be classified into Class I TEs orretrotransposons and Class II TEs or DNA transposons (Rodic et al, 2013).
Around 98% of the transposable elements are retrotransposons, which are againdivided into long terminal repeats (LTRs) or retrovirus that constitute of 8%of the human genome, and non-LTRs like long interspersed nuclear elements(LINEs) and short interspersed nuclear elements (SINEs), which are importantplayers in cancer. LINE1 sequences are almost 17% of the total human genome(Rodic et al, 2013). LINE 1 can copy and paste into a new gene location anddisrupt the gene expression of the associated gene and might be associated withoncogenic expression leading to cancer initiation (Bratfhaueret al, 1993; Carreira et al, 2013). LINE elements arefound in large number in the human genome.
These elements spans around 6-8 kband lack long terminal repeats. LINEs are rich in adenine residues at the 3’end. LINE is further subdivided into L1, L2 and L3.
L1 are activeretrotransposons and L2 and L3 are inactive ones (Miousse et al, 2015). LINE 1 spansaround 6-8 kb long and consists of RNA polymerase III promoter, 5′ untranslatedregion, two non- overlapping open reading frames (ORF1 and ORF2), and 3’untranslated region and flanked by target-specific direct repeats on the ends.ORF1 and ORF2 span approximately 1 kb and around 4 kb respectively (Refer fig.1). ORF1 encodes RNA-binding protein whose molecular weight is approximately 40kDa and on the other hand ORF2 encodes 150 kDa protein with the functionalactivities of endonuclease and reverse transcriptase (Refer fig. 1)(Li et al,2014). The studies show that these two proteins ORF1p and ORF2p are importantfor the retrotransposition (Luca et al, 2015).
Short interspersednuclear elements (SINEs) belong to non- Long Terminal Repeat group. They arenon-autonomous retrotransposons and comprise of approximately 13% of the humangenome. These elements are around 100-400 base pairs long. They often containRNA polymerase III promoters but no genes.
They do not code for reversetranscriptase and depend on other transposable elements for the transposition.Alu elements are the most common SINEs.Theretrotransposition mechanismThe mechanism ofretrotransposition is quite understood but has to be studied more to reveal themissing links and the underlying molecular mechanisms (Lee et al, 2012).
The twoproteins encoded by L1, which are ORF1p and ORF2p, are necessarily required forretrotransposition (Refer Fig. 2) (Wallaceet al, 2008). The integrasewhich is endonuclease create a two single strand breaks which appears to bedouble strand breaks at the integration site, which is AT rich DNA targetregion (Symer DE, 2002; Gasior et al, 2006). Following this step, the RNA transcript of the transposable element getsintegrated in the new location.
It acts as a primer for the reversetranscriptase and copies RNA into cDNA (Refer Fig 2). The other end of the DNAis joined and the important player is unknown. It is presumably detected andrepaired by DNA repair mechanism. But successful retrotransposition might posea great threat and can cause human diseases. It affects in the processes likeapoptosis and cell proliferation (Belgnaoui et al, 2006). The integration ofL1 may cause a risk of mutation, recombination, insertion, deletion leading togenomic instability. The insertion of L1 to the new site may likely to changethe function and nature of the gene. It can also lead to change in theexpression pattern of that particular gene- up-regulation or down-regulationwhich is responsible for the initiation of the disease (Kemp et al, 2015).
TranscriptionalderegulationRetrotransposonsare mobile elements and can get integrated anywhere in the whole genome. Theirinsertion in regulatory region of the gene can cause the transcriptionalderegulation (Rebollo, R 2012). The geneexpression pattern might change and hence the transcription level changes. Theup-regulation or down-regulation of the gene leads to the deregulation andcauses the human diseases. These elements get inserted in exons,introns, promoters, enhancers or silencers and may cause their defect.
Theintegration of these elements in exons can cause missense mutation, nonsensemutation and splice site mutations (Sela,N, 2010). Their insertion can also lead to the change in theopen reading frame and affect the transcription. The splice site can also getaffected and abruptly occur the new splice site. The introduction of Aluelements in the introns alters the alternative splice site (Lev-Maor, G, 2003, Lev-Maor,G, 2008). The introduction of the transposableelement can cause frameshift mutation or premature stop codon. These aboveevents lead to transcriptional deregulation. GenomicinstabilityThe genomicinstability is the hallmark of the cancer.
There are multifactorial reasons forthe genomic instability. There are DNA repair machinery and immune system whichare at their work all the time. But sometimes they fail to do their work andlead to havoc in the molecular machinery leading to deregulation andmismanagement. Theretrotransposons forms the major of transposable elements and are interestingto study because of their activity. LINE 1 elements encode two proteins ORF1p(RNA binding protein and ORF2p (endonuclease and reverse transcriptase) whichare thought to be important for their insertion in the new location. Theseelements are mobile and can be inserted inversely or in any random way. Theirintegration can cause mutation or rearrangements or recombinations (Pal et al,2011).
These events lead to chromosomal rearrangements and genomic instability (Choiet al, 2007; Ogino et al, 2008). LINE1elements get inserted in introns or in microsatellite repeats. Themicrosatellite instability is also responsible for cancer initiation (Inamuraet al, 2014). There are various studies showing microsatellite instability incancer progression (Marcos R. H. Este´cio et al, 2007). Microsatelliteinstability is an important feature of several colorectal, stomach, endometrium,ovary, urinary tract, skin, and brain cancers (Menendez et al, 2007; Negrini, S,2010; Baba et al, 2010; Anwar, 2017).
Insertion of transposable elements isknown to alter the transcription pattern of the target gene. We have discussedthis in previous paragraph. During replication and transcription, DNA repairsystem works but due to their inability, chances of DNA damage increases (Negrini,S, 2010). The DNA damage and transcriptional deregulation are responsible forgenomic instability and hence the cancer (Valeri, N,2010; Conti, A.; Carnevali, 2015; Daskaloset al 2009; Wolff et al, 2010; Belancio et al, 2010b). Carcinogenesis elements are present in the whole genome andare more supposed to more than 45% of the genome.
Earlier till their discovery,they were considered as junk DNA. But their discovery witnessed the phenomenalevent: they can transfer anywhere in the whole genome. The retrotransposons,which include LINE 1 and Alu elements, transfer as RNA transcript. LINE1 isautonomous whereas Alu elements are non-autonomous depends on LINE 1 for theiractivity (Rodriguez et al, 2008). Due to stress and environmental change,the epigenetics of the genomic DNA changes in the individuals (Refer Fig. 3).
Especially methylation pattern of the genomic DNA alters and increases thechance of human diseases. Several studies have shown that hypomethylation ofLINE1 causes the initiation and progression of the cancer. Hypomethylation ofLINE1 reactivates the LINE 1 and encodes for ORF1p (RNA binding protein) andORF2p (Endonuclease as well as Reverse transcriptase) (Refer Fig. 3). Theseelements then get inserted into their target region by creating double strandbreak by the endonuclease of LINE 1 (Gasioret al, 2006). The RNA transcript of L1 gets inserted andchanges the transcription pattern of the target gene (Refer Fig. 2). That alsoled to genomic instability, transcriptional deregulation, recombination,mutations and DNA damage (Schulzet al, 2005; Belancio et al, 2010b; Pal et al, 2011) (Refer Fig.
3). Theretrotransposition of the retrotransposons in the target gene disrupts itstranscriptional regulation (Lee et al, 2012) (Refer Fig. 3). The up-regulationor down-regulation of the gene affects the signalling pathway in which theparticular protein is involved. This event might activate oncogene or represstumor suppressor gene and initiate the cancer (Tufarelli et al, 2013).Various cancers have caused due tohypomethylation of the LINE 1. L1Hs expression leads to origin and progressionof some breast cancer (Bratteayr et al, 1994).
LINE 1 hypomethylation was morepronounced in higher stage carcinomas and was observed in lymph node positiveprostate carcinomas (Florl et al 2004). Thelevel of LINE-1 methylation in normal colonic mucosa is inversely associatedwith CpG island methylation (Iacopetta et al, 2007) and is associated withshorter survival of the patients (Oginoet al 2008). Inhepatocellular carcinomas, hypermethylation of CpG islands, and CpG islandmethylator phenotype status seems to correlate with levels of long interspersednuclear element-1 hypomethylation (Kimet al 2009). DNA hypomethylation changes occur later in prostatecarcinogenesis than the CpG island (Florl et al 2004; Yegnasubramanian et al2008). Renal cancers in particularappear to lack LINE-1 hypomethylation (Liao et al, 2011). Clinicaltrials will determine whether changes in LINE-1 methylation in plasmaDNA occur as a result of treatment with DNA methylation inhibitors and parallelchanges in tumor tissue DNA (Aparicio et al 2009).
Theresults showed a clear and significant linear correlation of progression ofloss of methylation LINE-1 element to progression of colorectal cancer disease(Sunami et al, 2011; Di et al, 2011).LINE1 hypomethylationmay be an important biomarker of bladder cancer risk, especially amongst women(Wilhelm et al, 2010; Wolff et al, 2010). GlobalDNA hypomethylation has been associated with the risk of cancers of the bladderand head/neck (Kitkumthorn et al, 2012). The strong correlation between LINE-1methylation levels among affected father-affected son pairs suggests thattransgenerational inheritance of an epigenetic event may be associated withdisease risk (Mirabello et al, 2010). LINE-1 hypomethylation was an independentmarker of poor prognosis in stage IA non-small cell lung cancer (Saito et al,2010). ConclusionLINE-1 methylation could be a useful biomarkerfor predicting the prognosis of the disease like cancer (Aparicio et al, 2009; Igarashiet al, 2010; Bae et al, 2011; Tufarelli et al, 2013). The 5-FU-mediatedinduction of phospho-histone H2A.
X, a marker of DNA damage, was inhibited byknockdown of LINE-1. These results suggest that LINE-1 methylation is a novelpredictive marker for survival benefit from adjuvant chemotherapy with oralfluoropyrimidines in colorectal cancer patients. This finding could beimportant for achieving personalized chemotherapy (Kawakami et al, 2010). Furtherstudies are needed to assess the potential of LINE-1 methylation status as aprognostic biomarker for young people with CRC (Antelo et al, 2012; Kaneko et al, 2016).LINE-1 hypomethylation in gastric cancer is associated with shorter survival,suggesting that it has potential for use as a prognostic biomarker (Xiang etal, 2011; Shigaki et al, 2012).
In summary, TEs are junk DNA but they arefound to play a big role in human diseases like cancer. LINE 1 gets reactivatedin most of the cancers. The epigenetic modification of retrotrotransposonsactivates the LINE 1 and further activates the key players in the cancer.However, less is known about the molecular mechanism underlying the initiationand progression of the cancer by the epigenetic modification ofretrotransposons. The epigenetic inhibitors can be used as drug targets oncethe mechanism is understood.