User:HadrienAnne/mir-196

miR-196 is a non-coding RNA called a microRNA that has been shown to be expressed in numerous animal species including vertebrates and invertebrates (miRBase.org) [1,2]. There are three paralogues of miR-196 in most vertebrate species : (e.g. mir-196a-1, mir-196a-2 and mir-196b in mouse and human). Some animals such as zebrafish have five paralogues while some animals appear to have only a single copy (Ciona intestinalis). MiR-196 appears to be an olfactores specific microRNA (including urochordates and vertebrates) and has now been predicted or experimentally confirmed in a wide range of species (MIPF0000031). miR-196 appears to be expressed from intergenic regions in HOX gene clusters. The hairpin precursors are predicted based on base pairing and cross-species conservation. In this case the mature sequence is excised from the 5' arm of the hairpin.

It has been suggested that a rare SNP (rs11614913) that overlaps hsa-mir-196a2 has been found to be associated with non-small cell lung carcinoma.

Species Distribution
mir-196 is highly conserved in a wide range of animals including the urochordate Ciona intestinalis and all vertebrates investigated thus far (mirbase link)

Currently these are species where the gene mir-196 was sequenced : carolina anole (Anolis carolinensis), Geoffroy's spider monkey (Ateles geoffroyi), cattle (Bos taurus), common carp (Cyprinus carpio), dog (Canis familiaris), chinese hamster (Cricetulus griseus), zebrafish (Danio rerio), horse (Equus caballus), Fugu rubripes (Japanese pufferfish), chicken, Western gorilla (Gorilla gorilla), human, brown woolly monkey (Lagothrix lagotricha), gray short-tailed opossum (Monodelphis domestica), rhesus macaque (Macaca mulatta), mouse, platypus (Ornithorhynchus anatinus), Japanese killifish (Oryzias latipes), sea lamprey (Petromyzon marinus), bonobo (Pan paniscus), Bornean orangutan (Pongo pygmaeus), common chimpanzee (Pan troglodytes), rat, pig, Zebra Finch (Taeniopygia guttata), Tetraodon nigroviridis and Western clawed frog (Xenopus tropicalis). As well as Ciona intestinalis (sea squirt), Myxine glutinosa (atlantic hagfish), Scyliorhinus canicula (catshark), lampetra planeri (river lamprey).

MiR-10 is conserved among protostomes and deuterostomes, MiR-615 is conserved among eutherian mammals, MiR-iab-4/miR-iab-8 are conserved among arthropods and are located between abd-A (Hox8) and Abd-B, MiR-4069 are located upstream of posterior Hox orthologues. In chick, the recently acquired and MiR-1732 is positioned adjacent to miR-196b in the HoxA cluster.

Genomic Locations
miR-196a-1 is located on chromosome 17 at a site between HOXB9 and HOXB10 genes. , miR-196a-2 is located on chromosome 12 at a site between HOXC10 and HOXC9 genes and miR-196b is located at a site between  HOXA9 and  HOXA10 genes on chromosome 7 in human and chromosome 6 in mice. .



miR-196a-1 and miR-196a-2 genes transcribe the same functional mature miRNA sequence whereas miR-196b gene produces a small RNA which differs from the sequence of miR-196a by one nucleotide.

Relation with other microRNA
The mir-196 family is one of eight other microRNA families located within the Hox clusters; mir-10, mir-196, mir-615, mir-993, mir-4069, mir-1991,mir-1732 and miR-iab-4/8 found in invertebrates such as Drosophila melanogaster, Apis mellifera and Bombyx mori. These 8 microRNA families are all located on the hox clusters and may have similar function. Hox genes encode homeodomain-containing transcription factors that are essential for embryonic development.



Relation with miR-10 family
(there is no direct relation to miR-10 aside from both being in the hox clusters... function and sequence are completely different)

Targets of miR-196
In ovo application of antagomiRs indicates a role for miR-196 in patterning the chick axial skeleton through Hox gene regulation. |journal=Proc Natl Acad Sci U S A |volume=106 |issue=44 |pages=18610–5 |year=2009 |pmid=19846767 |doi=10.1073/pnas.0910374106 |pmc=2773993}}. In zebrafish, miR-196 has been shown to regulate the axial skeleton through regulation of the Retinoic Acid pathway, resulting in loss or gain of extra rib-bearing vertebrae (He, et al. Dev Biol. 2011 Sep 15;357(2):463-77. doi: 10.1016/j.ydbio.2011.07.014. Epub 2011 Jul 20.)

Down-regulation of HOXB8, HOXC8, HOXD8 and HOXA7 and also cleavage mechanism for miR-196-directed repression of HOXB has been demonstrated by cell culture experiments. In ovo knockdown of miR-196 on chick resulted in highly significant posteriorizing transformation of the last cervical vertebra (C14).

MiR-196 repressed the expression of HOXB8 by cleaving the mRNAs and also regulates the expression of HOXC8, HOXD8 and HOXA7 by transcriptional inhibition.

HMGA2 gene is a target of miR-196a-2 which up-regulate miR-196a-2 expression and HMGA1 can down-regulate the expression of HMGA family members

Prediction targets
Several other genes have been predicted to be targeted by miR-196, including S100 calcium-binding protein A9, small proline-rich protein 2C, keratin 5, CLCA family member 2 (a chloride channel regulator), cytochrome P450 (family 4, subfamily B, polypeptide 1), keratin 4, LDOC1, leukotriene A4 hydrolase, pleiotrophin, T-cell differentiation protein, tumour protein D52-like 1, visinin-like 1 and v-ETS erythroblastosis virus E26 oncogene homologue (ERG). However, most of these target molecules of miR-196 have not been confirmed with experimental approaches

Role in developement
miR-196 appears to play an important role in development :


 * In Drosophila, there is a conserved or possibly convergent interaction between the miR-196 homologue iab-4 and the homeotic Ubx HOX gene.
 * In chicken, the interaction between miR-196 and HOXB8 is implicated in the mechanism that prevents the mesoderm to do limb induction by retinoic acid.


 * miR-196 target at the upstream of HOXB8 and Sonic hedgehog (Shh) in the context of limb development, specifically in the hindlimb..


 * The overexpressed of mir-196a induces eye anomalies in Xenopus laevis.

HMGA are nuclear architectural factors that play critical roles in a wide range of biological processes. Two variants of HMGA proteins, HMGA1 and HMGA2, have been identified[45]. Both HMGA genes are highly expressed during embryogenesis, and there is evidence that the absence of HMGA 2 protein causes growth retardation in mice.


 * HMGA1 is to regulate miR-196 expression, whereas miR-19a can control HMGA2 mRNA translation, which may affect development.

Precise levels of mir196 are required to initiate development of the pectoral appendage, to develop the correct number of pharyngeal arches, and to specify the number and identity of rostral vertebrae and ribs. We show that miR-196 can alter hox gene expression patterns and that miR-196 acts on pectoral appendage development by altering retinoic acid signaling via fine-tuning the expression of the retinoic acid receptor Rarab.

In developing embryos, miR-196 acts to modulate Hoxb8 levels both within. and immediately posterior to its endogenous expression domain in the paraxial mesoderm, and the detection of Hoxb8 endonucleolytic cleavage products in posterior regions. .

Role in morphognenesis
Although Hox genes chromosomal organization induces the graded expression of its genes through the anterior-posterior axis, this graded expression does not precisely align with the somites boundaries. The miR-196 plays a role in aligning and sharpening the expression of Hox genes through translation inhibition and mRNA cleavage. Differential miR-196 expression in hindlimb and forelimb has also been observed in chick and mouse (observed level of miR-196 20 fold greater in hindlimb than in forelimb). Because miR-196 downregulate HOXB8 which in turn induces Sonic Hedgehog, miR-196 is responsible of the differential expression of Sonic Hedgehog between the hindlimb and the forelimb. These observations ascribes the role of a safeguard for Hox genes expression to the miR-196. The role of miR-196 in axolotls tail regeneration has also been documented.

Role in cancer
Mir-196 can regulate cellular functions such as proliferation, apoptosis and differentiation.

Pancreatic cancer
The miRNA-196a levels are inversely correlated with survival in pancreatic adenocarcinoma patients. Up-regulation of miR-196a has also been found in pancreatic cancer. Thus, miR-196a can be used to diagnose pancreatic cancer by raising the level in cells.

Breast cancer
Up-regulation of miR-196a has also been found in breast cancer. This included up-regulation of previously reported breast cancer-related miRNAs such as miR-21, miR-155, miR-191 and miR-196a. The miR-196 family could suppress breast cancer cell migration and metastasis by inhibiting HOXC8 expression.

Leukaemia
In leukaemia, levels of miR-10a, miR-10b and miR-196a-1 showed a correlation with HOX gene expression (for 30 patients with leukemia). As the overexpression of a specific subset of the Hox genes is known to be a hallmark for the Mixed-Lineage Leukemia, the role of mir-196 in this pathology has been investigated. The MLL gene regulates expression during stem cell differentiation. In the pathological context of Mixed-Lineage Leukemia, the MLL protein is altered and induces the overexpression of mir-196. This overexpression of miR-196b was found specifically in patients with MLL-associated leukaemia (for 55 patients) Leukemogenic MLL fusion proteins cause overexpression of miR-196b, which may be necessary for MLL fusion-mediated immortalization. miR-196b expression is significantly more up-regulated in AML than ALL and that, again, miR-196b up-regulation is negatively associated with overall survival of  AML patients. Research of the expression of miR-196 in mouse's hematopoeitic progenitors has shown that miR-196 is expressed in long-term hematopoeitic stem cells (LT-HSC), short-term hematopoeitic stem cells (ST-HSC) and multipotent progenitors (MPP). Expression levels of mir-196b are the highest in ST-HSC and decrease as cells differentiates. In a physiological context, LT-HSCs become ST-HSCs, then MPP, then differentiated cells as the level of miR-196 decreases. In a physiological context, the high level of miR-196 increase survival and proliferation of ST-HSC and MPP and inhibits their differentiation.


 * The up regulation of mir-196b leads DNA methylation at CPg islands in the promoter regions of mir-196.
 * High expression of miR-196b causes leukemia.

Other tumors
miR-196b is known to induce changes in myeloid development, and the co-expression of miR-196b and miR-21 reportedly block granulocyte colony-stimulating factor-induced granulopoiesis completely. Highly elevated levels of miR-196a have also been detected in oesophageal adenocarcinoma. miR-196a may have growth-promoting and antiapoptotic functions. The expression of HMGA proteins is in general low or absent in normal tissues but overexpressed of HMGA proteins is observed in tumor cells of several  cancers, however, it was noted that mir-196 inhibits the synthesis of protein HMGA so it could inhibit tumor progression.

Oncogenic function
miR-196 has oncogenic function in cancer, it is important to point out that miR-196 may play a tumour suppressive role as well. miR-196 has a dominant effect on the inhibition of oncogenic molecules so miR-196 will play a tumour suppressor function.

stomach cancer
The expression levels of miR-196 in the gastric mucosa are higher in healthy patients than patients with intesinal cancer. SHH is downregulation by miR-196 in intestinal metaplastic glands in tumor tissues.

pancreatic cancer
miR-196a is up-regulated in pancreatic cancer.

glioblastoma
miR-196a is up-regulated in glioblastoma.

melanoma
miR-196a is down-regulated in melanoma, and its expression inhibits the invasion of melanoma cells by targeting HOXC8.

Other roles
MiRNA-196 appears to have several important cellular functions in addition to development and malignancy. Endometriosis is a gynaecological disorder in females in which endometrial-like cells grow in areas outside the uterine cavity. ..

miR-196 may also play a role in the pathogenesis of severe congenital neutropenia (SCN), a rare haematological disorder characterized by an abnormally low number of neutrophils Gfi1 is a transcriptional repressor that is required for normal myelopoiesis. It has been shown that miR-196b is negatively regulated by Gfi1. . miR-196 also has biological functions involving immunology, inflammation and virus defence. CD56+ T cells may be able to up-regulate the expression of miR-196a, showing in a study about hepatitis C virus (HCV). .

Overexpression of these miRNAs in infected liver cells leads to a marked attenuation of viral replication, demonstrating the importance of miRNAs in anti-viral immunity.

Since viruses also play a role in the pathogenesis of several tumour types, miRNAs may mediate viral–host interactions that have important implications not only for infectious diseases but also for cancer pathogenesis. The overexpression of miR-196a inhibited the proliferation of human adipose tissue-derived mesenchymal stem cells while enhancing osteogenic differentiation. . Finally, miR-196a may be used to storage of blood.

Role in limb regeneration
Experiments on axolotl tail regeneration has shown that miR-196 (at least indirectly) downregulates the expression of Pax7, BMP4 and Msx1 (those genes are involved in maintaining dorsal cell identity). On the other hand, these experiments have also shown that levels of Meis2 (an atypical homeobox domain protein playing a role in defining proximo-distal identity during limb regeneration) are significantly lowered in inhibitor-196-treated axolotls. According to these experiments, Meis2 and miR-196 may play a role in axolotl limb regeneration by determining positional identity and translating the information of "how much is to be regenerated yet".

HCV infection
miR-196 binding sites in the 3′-UTR of Bach1, which lead to down-regulation of Bach1 gene expression, up-regulation of HMOX1 gene expression, and down-regulation of HCV expression. .

Crohn’s disease
miR-196, is overexpressed in the inflammatory intestinal epithelia of individuals with Crohn’s disease and downregulates the IRGM protective variant (c.313C) but not the risk-associated allele (c.313T). Subsequent loss of tight regulation of IRGM expression compromises control of intracellular replication of Crohn’s disease–associated adherent invasive Escherichia coli by autophagy The human IRGM is currently a poorly understood regulator of Xenophagy, a dedicated form of Autophagy that engulfs and degrades intracellular pathogens as a host-defense mechanism.

miR-196 binding in the open reading frame of IRGM, an interaction whose misregulation may underly susceptibility to Crohn’s disease.