Editing Alu element (section)

== <span id="The Alu family"></span>Alu family ==
The Alu family is a family of repetitive elements in [[primate]] genomes, including the [[human]] [[genome]].<ref>{{Cite journal|last1=Arcot|first1=Santosh S.|last2=Wang|first2=Zhenyuan|last3=Weber|first3=James L.|last4=Deininger|first4=Prescott L.|last5=Batzer|first5=Mark A.|date=September 1995|title=Alu Repeats: A Source for the Genesis of Primate Microsatellites|journal=Genomics|volume=29|issue=1|pages=136–144|doi=10.1006/geno.1995.1224|pmid=8530063|issn=0888-7543}}</ref> Modern ''Alu'' elements are about 300 [[base pair]]s long and are therefore classified as [[short interspersed nuclear element]]s (SINEs) among the class of repetitive RNA elements. The typical structure is 5' - Part A - A5TACA6 - Part B - PolyA Tail - 3', where Part A and Part B (also known as "left arm" and "right arm") are similar nucleotide sequences.  Expressed another way, it is believed modern ''Alu'' elements emerged from a head to tail fusion of two distinct FAMs (fossil antique monomers) over 100 million years ago, hence its dimeric structure of two similar, but distinct monomers (left and right arms) joined by an A-rich linker. Both monomers are thought to have evolved from 7SL, also known as [[SRP RNA]].<ref name=pmid17020921>{{cite journal |doi=10.1093/nar/gkl706 |pmid=17020921 |pmc=1636486 |title=Alu elements as regulators of gene expression |journal=Nucleic Acids Research |volume=34 |issue=19 |pages=5491–7 |year=2006 |last1=Häsler |first1=Julien |last2=Strub |first2=Katharina }}</ref> The length of the polyA tail varies between ''Alu'' families.

There are over one million ''Alu'' elements interspersed throughout the human genome, and it is estimated that about 10.7% of the human genome consists of ''Alu'' sequences. However, less than 0.5% are [[Polymorphism (biology)|polymorphic]] (i.e., occurring in more than one form or morph).<ref name=pmid11560904>{{cite journal |pmid=11560904 |pmc=1461783 |year=2001 |last1=Roy-Engel |first1=A. M |title=Alu insertion polymorphisms for the study of human genomic diversity |journal=Genetics |volume=159 |issue=1 |pages=279–90 |last2=Carroll |first2=M. L |last3=Vogel |first3=E |last4=Garber |first4=R. K |last5=Nguyen |first5=S. V |last6=Salem |first6=A. H |last7=Batzer |first7=M. A |last8=Deininger |first8=P. L |doi=10.1093/genetics/159.1.279 }}</ref> In 1988, [[Jerzy Jurka]] and [[Temple Smith]] discovered that ''Alu'' elements were split in two major subfamilies known as AluJ (named after Jurka) and AluS (named after Smith), and other Alu subfamilies were also independently discovered by several groups.<ref name=pmid3387438>{{cite journal |doi=10.1073/pnas.85.13.4775 |pmid=3387438 |pmc=280518 |title=A fundamental division in the Alu family of repeated sequences |journal=Proceedings of the National Academy of Sciences |volume=85 |issue=13 |pages=4775–8 |year=1988 |last1=Jurka |first1=J |last2=Smith |first2=T |bibcode=1988PNAS...85.4775J |doi-access=free }}</ref> Later on, a sub-subfamily of AluS which included active Alu elements was given the separate name AluY. Dating back 65 million years, the AluJ lineage is the oldest and least active in the human genome. The younger AluS lineage is about 30 million years old and still contains some active elements. Finally, the AluY elements are the youngest of the three and have the greatest disposition to move along the human genome.<ref name=pmid18836035>{{cite journal |doi=10.1101/gr.081737.108 |pmid=18836035 |pmc=2593586 |title=Active Alu retrotransposons in the human genome |journal=Genome Research |volume=18 |issue=12 |pages=1875–83 |year=2008 |last1=Bennett |first1=E. A |last2=Keller |first2=H |last3=Mills |first3=R. E |last4=Schmidt |first4=S |last5=Moran |first5=J. V |last6=Weichenrieder |first6=O |last7=Devine |first7=S. E }}</ref> The discovery of ''Alu'' subfamilies led to the hypothesis of master/source genes, and provided the definitive link between transposable elements (active elements) and interspersed repetitive DNA (mutated copies of active elements).<ref name=pmid1774786>{{cite journal |doi=10.1007/bf02102862 |pmid=1774786 |title=Evolution of the master Alu gene(s) |journal=Journal of Molecular Evolution |volume=33 |issue=4 |pages=311–20 |year=1991 |last1=Richard Shen |first1=M |last2=Batzer |first2=Mark A |last3=Deininger |first3=Prescott L |bibcode=1991JMolE..33..311R |s2cid=13091552 }}</ref>

=== Related elements ===
B1 elements in rats and mice are similar to Alus in that they also evolved from 7SL RNA, but they only have one left monomer arm. 95% percent of human Alus are also found in chimpanzees, and 50% of B elements in mice are also found in rats. These elements are mostly found in introns and upstream regulatory elements of genes.<ref>{{cite journal |last1=Tsirigos |first1=Aristotelis |last2=Rigoutsos |first2=Isidore |last3=Stormo |first3=Gary D. |title=Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes |journal=PLOS Computational Biology |date=18 December 2009 |volume=5 |issue=12 |pages=e1000610 |doi=10.1371/journal.pcbi.1000610 |pmid=20019790 |pmc=2784220|bibcode=2009PLSCB...5E0610T |doi-access=free }}</ref>

The ancestral form of Alu and B1 is the fossil Alu monomer (FAM). Free-floating forms of the left and right arms exist, termed free left Alu monomers (FLAMs) and free right Alu monomers (FRAMs) respectively.<ref>{{cite journal |last1=Kojima |first1=K. K. |title=Alu Monomer Revisited: Recent Generation of Alu Monomers |journal=Molecular Biology and Evolution |date=16 August 2010 |volume=28 |issue=1 |pages=13–15 |doi=10.1093/molbev/msq218 |pmid=20713470|doi-access=free }}</ref> A notable FLAM in primates is the [[BC200 lncRNA]].