HHV Latency Associated Transcript
HHV Latency Associated Transcript (HHV LAT) is a length of RNA which accumulates in cells hosting long-term, or latent, Human Herpes Virus (HHV) infections. The LAT RNA is produced by genetic transcription from a certain region of the viral DNA. LAT regulates the viral genome and interferes with the normal activities of the infected host cell.
Herpes virus may establish life-long infection during which a reservoir virus population survives in host nerve cells for long periods of time. Such long-term Herpes infection requires a mode of cellular infection known as latent infection. During the latent infection, the metabolism of the host cell is disrupted. While the infected cell would ordinarily undergo an organized death or be removed by the immune system, the consequences of LAT production interfere with these normal processes.
Latency is distinguished from lytic infection; in lytic infection many Herpes virus particles are produced and then burst or lyse the host cell. Lytic infection is sometimes known as "productive" infection. Latent cells harbor the virus for long time periods, then occasionally convert to productive infection which may lead to a recurrence of symptomatic Herpes symptoms.
During latency, most of the Herpes DNA is inactive, with the exception of LAT, which accumulates within infected cells. The region of HHV DNA which enodes LAT is known as LAT-DNA. After splicing, LAT is a 2.0-kilobase transcript (or intron) produced from the 8.3-kb LAT-DNA. The DNA region containing LAT-DNA is known as the Latency Associated Transcript Region. 
Apoptosis is the process of normal cell death. In order to maintain a reservoir of latently infected host cells, Herpes virus interferes with apoptosis. HSV-1 LAT expression produces interfering micro-RNA (miRNA) which suppress production of Human apoptosis-pathway proteins such as TGF-β1 and SMAD3.  HHV-8 LAT expression similaraly produces miRNAs which suppress production of Thrombospondin-1 protein involved in apoptosis and angiogenesis.  Expression of LAT also reduces the production of other proteins invovled in the apoptosis mechanism, including proteins caspase-8 and caspase-9. 
LAT expression regulates the activity of the Herpes genome during latent infection. LAT expression results in the suppression of Herpes lytic genes.  Genetic studies of the LAT-DNA have identified a portion known as a chromatin insulator which forms a boundary between activated LAT-DNA and the inactive lytic viral DNA. 
LAT regulates the expression of lytic genes
HHV Infected Cell Polypeptide 0 (ICP0) gene is expressed very early during lytic infection, and for this reason is called an immediate-early Herpes gene. In 1991, Farrell and colleagues report that the 2.0-kb LAT intron terminates at the 5' end with a 750-base antisense RNA complement for the ICP0 gene. 
In 2005, Quing-Yin Wang and colleagues from Harvard Medical School concluded, using assays comparing LAT-negative vs. LAT-positive virus strains, that expression of LAT in neurons represses the expression of several lytic gene products, including ICP4 and Thymidine Kinase. LAT expression results in changes to Histones, thus converting portions of viral DNA into a non-productive form known as heterochromatin. 
Simian Varicella Virus (SVV) is a Varicellovirus (a Genus of Subfamily Alphaherpesvirinae) which expresses an HHV LAT homolog known as SVV LAT, and an HHV ICP0 analog known as SVV-ORF61 (Open Reading Frame). SVV LAT is encoded such that it contains an antisense copy of SVV-ORF61 and that expression of SVV LAT during latency downregulates expression of ORF61 and other immediate-early SVV gene products.
LAT DNA contians an activation boundary called a chromatin insulator
CCCTC-binding factor (CTCF) is a zinc finger protein which occurs naturally in some human cells. CTCF is localized to the nucleus of cells. CTCF has been shown  to naturally regulate the expression of human linear dsDNA by binding with target DNA sequences or motifs. CTCF binding to DNA may result in formation of transcription-ready euchromatin through the Histone H3-acetylating activity which results due to CTCF binding. Acetylation of Histone promotes transcription of DNA to RNA, and then to protein products.
A March 2006 University of Florida College of Medicine study showed that expression of the Herpes virus genome may be regulated in part by the binding of CTCF to CTCF-binding motifs. The researchers used sequence analysis and quantitative genomics assays on HHV DNA. In the U. Florida study, the LAT region was found to contain a CTCF-binding region within a 1.5k-bp (base pair) region, and found to contain a "chromatin insulator-like element". A May 2007 study conducted at the Wistar Institute localized the LAT CTCF-binding motif to an 800-bp sequence of the LAT intron, and demonstrated that the region insulated activated LAT chromatin from repressed chromatin that would otherwise produce the lytic protein HHV Infected Cell Polypeptide 0 (ICP0).
LAT miRNA interferes with host cell apoptosis
Research has shown that a portion of HSV-1 LAT consists of an interfering micro RNA (miRNA). This miRNA was termed miR-LAT, and shown to downregulate Transforming Growth Factor-β1 (TGF-β1) and SMAD3. These effects block apoptosis, or normal programmed cell death.  Further research has shown that HHV-8 LAT produces miRNA which interfere not with expression of TGF-β1 and SMAD3, but reducing the expression of Thrombospondin-1 protein (THBS-1). In turn, down-regulation of THBS-1 reduces production of TGF-β1 and SMAD3, suppressing apoptosis.
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- Chen Q, Lin L, Smith S, Huang J, Berger SL, Zhou J (May 2007). "CTCF-Dependent Chromatin Boundary Element between the Latency-Associated Transcript and ICP0 Promoters in the Herpes Simplex Virus Type 1 Genome". Journal of Virology. 81 (10): 5192-201. PMID 17267480.