28
Xenopus
TABLE 3.1
Selected Vegetally Localized mRNAs in Xenopus
Late Pathway mRNAs
Gene Symbol
References
growth differentiation factor 1 (alias vg1)
gdf1
Rebagliati et al., 1985; Weeks et al., 1987; Birsoy et al., 2006
vegt
vegt
Zhang and King, 1996; Zhang et al., 1998
acyl-CoA synthetase long-chain 1
acsl1b
King et al., 2005; Wang et al., 2012
bicaudal C homolog 1
bicc1
Wessely and Robertis, 2000; Park et al., 2016
low density lipoprotein receptor adaptor protein 1
ldlrap1
Zhou et al., 2004
orthodenticle homolog 1
otx1
Pannese et al., 2000; Owens et al., 2017; Paraiso et al., 2019
zinc f nger protein 36-like 2 (C3H-3)
zfp36l2
Betley et al., 2002
beta-transducin repeat containing E3 ubiquitin protein ligase
btrc
Hudson et al., 1996
ephrin-b1
efnb1
Betley et al., 2002; Owens et al., 2017
sox7
sox7
Claussen et al. 2015; De Domenico et al. 2015;
Early Pathway mRNAs
nanos homolog 1 (xcat2)
nanos1
Mosquera et al., 1993; Lai et al., 2012
deleted in azoospermia-like
dazl
Houston et al., 1998; Houston and King, 2000b
ddx25 (deadsouth)
ddx25
MacArthur et al., 2000; Yamaguchi et al., 2013
germes
germes
Berekelya et al., 2003
dead (Asp-Glu-Ala-Asp) box polypeptide 59 (centroid)
ddx59
Kloc and Chan, 2007
xpat/pgat
pgat
Hudson and Woodland, 1998
xsirt 13.2
xsirts
Kloc et al., 1993
proprotein convertase subtilisin/kexin type 6 (pace4)
pcsk6
Birsoy et al., 2005
syntabulin
sybu
Colozza and Robertis, 2014; Oh and Houston, 2017b
RAS related 2
rras2
Owens et al., 2017
Intermediate/Dual Pathway mRNAs
tripartite motif-containing protein 36
trim36
Cuykendall and Houston, 2009
wnt11b
wnt11
Ku and Melton, 1993; Kloc et al., 1998; Tao et al., 2005
perilipin 2 (alias fatvg)
plin2
Chan et al., 1999, 2007
DND microRNA-mediated repression inhibitor 1
dnd1
Weidinger et al., 2003; Mei et al., 2013
RNA binding protein with multiple splicing (alias hermes)
rbpms
Zearfoss et al., 2004
glutamate receptor interacting protein 2
grip2
Kaneshiro et al. 2007; Tarbashevich et al., 2007
low molecular weight neuronal intermediate f lament
nif
Claussen et al., 2004
vegetally-localized 1
velo1
Claussen and Pieler, 2004; Nijjar and Woodland, 2013b
Strategies for Identifying Maternally Localized mRNAs
Database
References
Animal/Vegetal Half RNA sequencing (8-cell stage)
GSE118024
Paraiso et al., 2019
Differential RNA sequencing/Proteomics
GSE104848
Sindelka et al., 2018
Differential RNA sequencing
GSE80971
Owens et al., 2017
Differential RNA sequencing
GSE58420
Claussen et al., 2015
Single blastomere RNA sequencing(8-cell stage)
N/A
De Domenico et al., 2015
Animal/Vegetal halves/Affymetrix microarray (8-cell stage)
GSE48659
Grant et al., 2014
Vegetal cortex isolation/Affymetrix microarray
GSE17713
Cuykendall and Houston, 2010
Differential hybridization to cDNA arrays
N/A
Horvay et al., 2006
Differential hybridization to cDNA arrays
N/A
Kataoka et al., 2005
Computational analysis of 3’UTRs
N/A
Betley et al., 2002
Differential display PCR
N/A
Hudson et al., 1996
Differential cDNA library screening
N/A
Zhang and King, 1996
Differential cDNA library screening
N/A
Rebagliati et al., 1985
loss of function, if available. Intermediate pathway RNAs
are defned as having mainly a late localization pattern
but with additional localization to the mitochondrial
cloud and to the germ plasm in embryos. Studies using
different molecular or “genomics” strategies to identify
vegetally localized mRNAs have increased in frequency
since 2014.
3.3. ANALYSIS OF MATERNAL GENE
FUNCTION IN XENOPUS DEVELOPMENT
The genetic assessment of maternally supplied gene
products in early development requires eggs derived
from a female lacking functional copies of the gene: a
“maternal effect” mutation. These analyses involve either