Biology Reference
In-Depth Information
Wheeler
et al
., 2009
). A similar genomic organization occurs in the annelid
Capitella
; based on comparison of the genomic locations of
miR-10
to those
for protein-coding Hox genes (
Frobius
et al
., 2008
;
Wheeler
et al
., 2009
),
copies are found between
Dfd
and
Scr
, between
lox5
/
ftz
and
Antp
, and 5
0
(distal) to
lox4
(
Ubx
). It is striking that these distantly related organisms show
such similar patterns of
miR-10
duplication.
Finally,
miR-993
is another
miR-10
/
miR-100
family member that proba-
bly arose as a duplication of
miR-10
early in the protostome lineage (
Griffiths-
Jones
et al
., 2011
).
miR-933
has been identified in multiple insect orders and
in the annelid
Capitella
, and it is located 3
0
(proximal) to
Hox4/Dfd
genes in all
species examined (
Marco
et al
., 2010
;
Ruby
et al
., 2007
;
Sperling
et al
., 2009
).
No functional studies of
miR-993
have yet been reported.
2.2.2.
miR-196
miR-196
likely arose in a common ancestor of chordates and urochordates.
It has been found in
Ciona,
in an agnathan (lamprey), and in all major groups
of gnathostomes (
Heimberg
et al
., 2010
;
Hendrix
et al
., 2010
;
Tanzer
et al
.,
2005
;
Yekta
et al
., 2004
). All known vertebrate
miR-196
genes are located
between
Hox9
and
Hox10
(
Fig. 2.1
)(
Heimberg
et al
., 2010
;
Tanzer
et al
.,
2005
;
Yekta
et al
., 2004
). It is notable that the
Amphioxus
genome, although
lacking
miR-196
, has a
miR-10
paralog between
Hox9
and
Hox10
, and some
invertebrate genomes also have a miRNA in a similar position. Together, this
suggests that selection for a miRNA in this genomic location may have arisen
prior to the evolution of
miR-196
itself.
Ciona miR-196
is not positioned near
Hox genes; however, the
Ciona
Hox cluster has been significantly rearranged
and dispersed (
Hendrix
et al
., 2010
;
Ikuta
et al
., 2004
).
miR-196
paralogs are locatedon the
Hoxa
-
c
clusters ofmost extant gnathos-
tomes, although losses have occurred particularly in teleosts (
Ravi
et al
., 2009
;
Tanzer
et al
., 2005
;
Yekta
et al
., 2004
). The
miR-196-5p
seed sequence is
perfectly conserved across vertebrates. To date, there is no evidence for
alternative posttranscriptional processing of
miR-196
as there is for
miR-10.
One variation of the genomic position of
miR-196
has been described:
in the amphibian
Xenopus tropicalis
, two of the three copies are located
within introns of
Hox9
genes. As described below,
miR-196
and
Hox9
are
cotranscribed in many vertebrates; however,
X. tropicalis
is only one known
in which the major
Hox9
transcripts, rather than rarer variants, appear to be
polycistronic (
Tang and Maxwell, 2008
).
2.2.3.
miR-iab-4/miR-iab-8
miR-196
is specific to chordates; however, a miRNA unrelated in sequence
occupies a similar position within the posterior Hox clusters of some
arthropods. This miRNA is transcribed from both DNA strands to generate
antisense
miR-iab-4
and
miR-iab-8
(also known as
miR-iab-4AS
) miRNAs.
miR
-
iab-4
has been identified in multiple insect orders and in the crustacean
