Transcript LINEs in Human Genome

LINEs and SINEs
….& towards cancer!
Presenter: Manindra Singh
Course: MCB 720 (Winter Qt.)
Overview
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LINEs ( Long Interspersed Elements) and
SINEs (Short Interspersed Elements)
are 2 classes of Non LTR Transposons, also called as nonviral retrotransposons
Non-LTR Retrotransposons transpose through an RNA intermediate utilizing a
reverse transcriptase and lack flanking terminal repeat sequence (LTRs).
•
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LINEs are ~ 6 Kb long, Observed in protozoans, insects, and plants.
Abundant in mammalian genomes
•
SINEs are ~ 300 bp long and are found primarily in mammalian DNA
LINEs in Human Genome

LINE sequences are present at ≈900,000 sites in the human genome.
Account for 21 % of total human DNA!

Human DNA contains three major families of LINE sequences:
L1, L2, and L3

L1, L2 and L3 LINE elements differ in their sequences, but mechanism of
transposition is similar, involving an RNA intermediate

Only members of the L1 family transpose in the contemporary human
genome
SINEs in Human Genome

Second most abundant class of mobile elements in the human genome

SINEs occur at about 1.6 million sites in the human genome, and constitute
≈13 percent of total human DNA

Most of the SINE sequences contain a single recognition site for the restriction
enzyme AluI (AGCT) and are called Alu elements - present in ~ 1.1 million
sites

Alu elements are scattered throughout the human genome: between genes,
within introns, and in the 3’UTRs of some mRNAs

Alu elements exhibit considerable sequence homology with 7SL RNA, a
component of the signal-recognition particle in the ER membrane
General Structure of a LINE
from Lodish et al., Molecular Cell Biology, 5th ed. Fig 10-15

LINEs are flanked by short direct repeats of variable length and
contain two long open reading frames (ORFs)
 ORF1, ≈1 kb in length, encodes an RNA-binding protein

ORF2, ≈4 kb in length, encodes a bifunctional protein with reverse
transcriptase and DNA endonuclease activity
Proposed Mechanism of LINE Transposition

Move by ‘copy & paste’ mechanism
LINE mRNA is transcribed by RNA Pol II, and directed by
promoter sequences at the left end of integrated LINE DNA


ORF1 and ORF2 proteins bind LINE mRNA &
mediate its’ nuclear transport
ORF2 catalyze its reverse transcription and
integration at A/T rich sites

SINEs are transcribed by RNA polymerase III, and
follow the same reterotransposition mechanism
mediated by ORF1 & ORF2 expressed from LINE RNA
from Lodish et al., Molecular Cell Biology, 5th ed. Fig 10-16
Mutations in LINEs reduce their efficiency of transposition

The vast majority of LINEs in the human genome are truncated at their 5’ end
due to erroneous nature of reverse transcription

The average size of LINE elements is only about 900 base pairs, whereas the
full-length sequence is ≈6 kb long

Only≈0.01 percent of the LINE sequences in the human genome are full-length
with intact ORF1 and ORF2, ≈60–100 in total!

Like LINEs, many SINEs also are truncated at their 5 end

SINEs also have accumulated mutations from the time of their insertion in the
germ line of an ancient ancestor of modern humans
NON-LTR ELEMENTS IN CANCER and TUMOR DEVELOPMENT

Mobile element insertion takes place at certain characteristic sites, some
corresponding to tumor suppressor genes e.g. APC (Adenomatous Polyposis Coli)

L1 retroelement integration into the tumor-suppressing gene APC has been found in
colon cancer patients

L1 retroelement insertion into the human protooncogene c-myc was found in human
breast cancinoma cells

Insertions of the Alu element into the intron of the NF-1 (neurofibromatosis type I)
gene may lead to neurofibromatosis

Ectopic recombination between Alu elements results in chromosomal aberrations,
associated with acute myeloid leukemia
L1 elements as cancer cell biomarkers

LINE-1 methylation is identified as a molecular marker of prognosis for CM
patients in stage IIIC (Sigalotti et. al, 2011)

L1 elements have been hypothesized as potential molecular marker in cancer
detection as L1 activity significantly increases in most human cancers
(Piskareva et. al, 2011)

Global hypomethylation in cells may trigger the activation of L1 element
expression which may cause activation of some proto-oncogenes
(Weber et. al, 2010)

L1 methylation pattern can be analyzed to study the degree carcinogenesis
(Aporntewan et. al.,2011)`
References
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Textbook : Molecular Cell Biology, Lodish et al., 6th ed.
Research articles:
1. Mobile genetic elements and cancer. From mutations to gene therapy. Kozeretska et. al. Exp Oncol
2011, 33, 4, 198–205.
2. Methylation levels of the “long interspersed nucleotide element-1” repetitive sequences predict
survival of melanoma patients. Sigalotti et al. Journal of Translational Medicine 2011, 9:78
3. The Human L1 Element: A Potential Biomarker in Cancer Prognosis, Current Status and Future
Directions. Piskareva et. al. Curr Mol Med. 2011, 11(4):286-303.
4. Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through
induction of illegitimate transcription. Weber et. al. Oncogene 2010, 29, 5775-5784.
5. Hypomethylation of Intragenic LINE-1 Represses Transcription in Cancer Cells through AGO2.
Aporntewan et. al. Plos One 2011, 6:3
6. Disruption of the APC Gene by a Retrotransposal Insertion of LI Sequence in a Colon Cancer. Miki,
Y. et. al. Cancer Reserch, 1992, 52, 643-645.