Analysis of Hox-4.5 and Hox-3.6 expression during newt limb regeneration: differential regulation of paralogous Hox genes suggest different roles for members of different Hox clusters

Development ◽  
1993 ◽  
Vol 117 (4) ◽  
pp. 1397-1407 ◽  
Author(s):  
H.G. Simon ◽  
C.J. Tabin
Keyword(s):  
Hox Genes ◽  
Limb Regeneration ◽  
Differential Regulation ◽  
Epithelial Tissue ◽  
Cdna Clones ◽  
Rnase Protection ◽  
Adult Kidney ◽  
Early Expression ◽  
Hox Clusters ◽  
Newt Limb

Adult urodele amphibians can regenerate their limbs and tail. Based on their roles in other developing systems, Hox genes are strong candidates for genes that play a role in regulating pattern formation during regeneration. There are four homologous clusters of Hox genes in vertebrate genomes. We isolated cDNA clones of two newt homeobox genes from homologous positions within two Hox clusters; Hox-4.5 and Hox-3.6. We used RNase protection on nonamputated (normal) and regenerating newt appendages and tissue to compare their transcriptional patterns. Both genes show increased expression upon amputation with similar kinetics. Hox-4.5 and Hox-3.6 transcription is limited to the mesenchymal cells in the regenerates and is not found in the epithelial tissue. In addition to regenerating appendages, both genes are transcriptionally active in adult kidney of the newt. Striking differences were found in the regulation of Hox-4.5 and Hox-3.6 when they were compared in unamputated limbs and in regenerating forelimbs versus regenerating hindlimbs. Hox-4.5 is expressed in the blastema of regenerating fore- and hindlimbs, but Hox-4.5 transcripts are not detectable in normal limbs. In contrast, Hox-3.6 transcripts are found exclusively in posterior appendages, but are present in normal as well as regenerating hindlimbs and tails. Hox-4.5 is also expressed at a higher level in proximal (mid-humerus) regenerates than in distal ones (mid-radius). When we proximalized the positional memory of a distal blastema with retinoic acid, we find that the early expression level of Hox-4.5 is also proximalized. When the expression of these genes is compared to the expression of two previously reported newt Hox genes, a consistent pattern emerges, which can be interpreted in terms of differential roles for the different Hox clusters in determining regenerative limb morphology.

Identification and expression of a regeneration-specific homeobox gene in the newt limb blastema

Development ◽  
1991 ◽  
Vol 111 (2) ◽  
pp. 489-496 ◽  
Author(s):  
R. Brown ◽  
J.P. Brockes
Keyword(s):  
Retinoic Acid ◽  
Amino Acid ◽  
Pattern Formation ◽  
Amino Acid Sequence ◽  
Homeobox Gene ◽  
Growth Zone ◽  
Epithelial Tissue ◽  
Cdna Clones ◽  
Time Points ◽  
Newt Limb

Adult urodele amphibians are able to regenerate their limbs through the formation of a blastema, a growth zone of undifferentiated mesenchymal cells that arises locally at the plane of amputation. In an effort to define genes involved in pattern formation by the blastema, we isolated from a newt forelimb blastema library cDNA clones that identify a homeobox gene termed NvHbox 2. The amino acid sequence of the homeodomain is identical to that of the recently identified human HOX-4f gene (Acampora et al. 1989) and of the mouse Hox-5.5 (Dolle et al. 1989). NvHbox 2 is expressed in the limb blastema as a transcript of 3.4 kb that is not detectable in the normal limb. Analysis by RNAase protection demonstrates expression in limb and tail blastemas, but not in any of the adult tissues or organs tested. In the limb blastema NvHbox 2 was expressed in mesenchymal but not epithelial tissue. When matched and normalised samples of RNA from proximal (mid-humerus) and distal forelimb (mid-radius) blastemas were compared, the level of expression of NvHbox 2 was found to be 3- to 5-fold higher proximally. At two time points after injection of a proximalising dose of retinoic acid, the level of expression in a distal blastema was not increased in comparison to controls.

Xenopus Distal-less related homeobox genes are expressed in the developing forebrain and are induced by planar signals

Development ◽  
1993 ◽  
Vol 117 (3) ◽  
pp. 961-975 ◽  
Author(s):  
N. Papalopulu ◽  
C. Kintner
Keyword(s):  
In Situ Hybridization ◽  
Neural Plate ◽  
Cdna Clones ◽  
Rnase Protection ◽  
Early Expression ◽  
Neural Ectoderm ◽  
Polymerase Chain ◽  
Sequence Similarities ◽  
Anterior Neural Plate

The polymerase chain reaction (PCR) was used to isolated five Xenopus homeobox clones (X-dll1 to 5) that are related to the Drosophila Distal-less (Dll) gene and we propose a subdivision of the vertebrate distal-less gene family according to sequence similarities. cDNA clones were isolated for X-dll2, 3 and 4, and their expression was studied by RNase protection and in situ hybridization. X-dll2, which belongs to a separate subfamily than X-dll3 and 4, is not expressed in the neural ectoderm. X-dll3 and X-dll4, which belong to the same subfamily, have a similar but not identical pattern of expression that is restricted to anterior ectodermal derivatives, namely the ventral forebrain, the cranial neural crest and the cement gland. X-dll3 is also expressed in the olfactory and otic placodes while X-dll4 is expressed in the developing eye. X-dll3 differs from the other Xenopus genes and the previously isolated Dll-related mouse genes, in that localized expression can be detected by in situ hybridization very early in development, in the anterior-transverse ridge of the open neural plate. Based on that early expression pattern, we suggest that X-dll3 marks the rostral-most part of the neural plate, which gives rise to the ventral forebrain. Finally, we have used these Xenopus distal-less genes to show that the anterior neural plate can be induced by signals that spread within the plane of neural ectoderm, indicating that at least the initial steps of forebrain development do not require signals from underlying mesoderm.

scholarly journals Normal newt limb regeneration requires matrix metalloproteinase function

2005 ◽  
Vol 279 (1) ◽  
pp. 86-98 ◽  
Author(s):  
Vladimir Vinarsky ◽  
Donald L. Atkinson ◽  
Tamara J. Stevenson ◽  
Mark T. Keating ◽  
Shannon J. Odelberg
Keyword(s):  
Matrix Metalloproteinase ◽  
Limb Regeneration ◽  
Newt Limb

scholarly journals The Role of the Prod1 Membrane Anchor in Newt Limb Regeneration

2016 ◽  
Vol 129 (1) ◽  
pp. 276-280
Author(s):  
Kaoru Nomura ◽  
Yasushi Tanimoto ◽  
Fumio Hayashi ◽  
Erisa Harada ◽  
Xiao-Yuan Shan ◽  
...  
Keyword(s):  
Limb Regeneration ◽  
Membrane Anchor ◽  
Newt Limb

scholarly journals Cloning and functional characterization of mammalian homologues of the COPII component Sec23.

1996 ◽  
Vol 7 (10) ◽  
pp. 1535-1546 ◽  
Author(s):  
J P Paccaud ◽  
W Reith ◽  
J L Carpentier ◽  
M Ravazzola ◽  
M Amherdt ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Gel Filtration ◽  
Apparent Molecular Weight ◽  
Cdna Clones ◽  
Restrictive Temperature ◽  
Rnase Protection ◽  
Cell Extracts ◽  
Exact Function ◽  
Mammalian Protein

We screened a human cDNA library with a probe derived from a partial SEC23 mouse homologue and isolated two different cDNA clones (hSec23A and hSec23B) encoding proteins of a predicted molecular mass of 85 kDa. hSec23Ap and hSec23Bp were 85% identical and shared 48% identity with the yeast Sec23p. Affinity-purified anti-hSec23A recognized a protein of approximately 85 kDa on immunoblots of human, mouse, and rat cell extracts but did not recognize yeast Sec23p. Cytosolic hSec23Ap migrated with an apparent molecular weight of 350 kDa on a gel filtration column, suggesting that it is part of a protein complex. By immunoelectron microscopy, hSec23Ap was found essentially in the ribosome-free transitional face of the endoplasmic reticulum (ER) and associated vesicles. hSec23Ap is a functional homologue of the yeast Sec23p as the hSec23A isoform complemented the temperature sensitivity of the Saccharomyces cerevisiae sec23-1 mutation at a restrictive temperature of 34 degrees C. RNase protection assays indicated that both hSec23 isoforms are coexpressed in various human tissues, although at a variable ratio. Our data demonstrate that hSec23Ap is the functional human counterpart of the yeast COPII component Sec23p and suggest that it plays a similar role in mammalian protein export from the ER. The exact function of hSec23Bp remains to be determined.

scholarly journals Two Alternatively Spliced Transcripts from the Drosophila period Gene Rescue Rhythms Having Different Molecular and Behavioral Characteristics

1998 ◽  
Vol 18 (11) ◽  
pp. 6505-6514 ◽  
Author(s):  
Yuzhong Cheng ◽  
Barbara Gvakharia ◽  
Paul E. Hardin
Keyword(s):  
Type A ◽  
Behavioral Characteristics ◽  
Cdna Clones ◽  
Type B ◽  
Differential Splicing ◽  
Rnase Protection ◽  
Period Gene ◽  
Alternatively Spliced ◽  
Transgenic Flies

ABSTRACT The period (per) and timeless(tim) genes encode key components of the circadian oscillator in Drosophila melanogaster. The pergene is thought to encode three transcripts via differential splicing (types A, B, and C) that give rise to three proteins. Since the threeper mRNA types were based on the analysis of cDNA clones, we tested whether these mRNA types were present in vivo by RNase protection assays and reverse transcriptase-mediated PCR. The results show that per generates two transcript types that differ only by the presence (type A) or absence (type B′) of an alternative intron in the 3′ untranslated region. Transgenic flies containing transgenes that produce only type B′ transcripts (perB′ ), type A transcripts (perA ), or both transcripts (perG ) rescue locomotor activity rhythms with average periods of 24.7, 25.4, and 24.4 h, respectively. Although no appreciable differences in type A and type B′ mRNA cycling were observed, a slower accumulation of PER in flies making only type A transcripts suggests that the intron affects the translation ofper mRNA.

Independent regulation of initiation and maintenance phases ofHoxa3expression in the vertebrate hindbrain involve auto- and cross-regulatory mechanisms

Development ◽  
2001 ◽  
Vol 128 (18) ◽  
pp. 3595-3607 ◽  
Author(s):  
Miguel Manzanares ◽  
Sophie Bel-Vialar ◽  
Linda Ariza-McNaughton ◽  
Elisabetta Ferretti ◽  
Heather Marshall ◽  
...  
Keyword(s):  
Hox Genes ◽  
Late Phase ◽  
General Mechanism ◽  
Chick Embryos ◽  
Early Expression ◽  
Horn Shark ◽  
Initial Activation ◽  
Group 3 ◽  
Regulatory Loop

During development of the vertebrate hindbrain, Hox genes play multiples roles in the segmental processes that regulate anteroposterior (AP) patterning. Paralogous Hox genes, such as Hoxa3, Hoxb3 and Hoxd3, generally have very similar patterns of expression, and gene targeting experiments have shown that members of paralogy group 3 can functionally compensate for each other. Hence, distinct functions for individual members of this family may primarily depend upon differences in their expression domains. The earliest domains of expression of the Hoxa3 and Hoxb3 genes in hindbrain rhombomeric (r) segments are transiently regulated by kreisler, a conserved Maf b-Zip protein, but the mechanisms that maintain expression in later stages are unknown. In this study, we have compared the segmental expression and regulation of Hoxa3 and Hoxb3 in mouse and chick embryos to investigate how they are controlled after initial activation. We found that the patterns of Hoxa3 and Hoxb3 expression in r5 and r6 in later stages during mouse and chick hindbrain development were differentially regulated. Hoxa3 expression was maintained in r5 and r6, while Hoxb3 was downregulated. Regulatory comparisons of cis-elements from the chick and mouse Hoxa3 locus in both transgenic mouse and chick embryos have identified a conserved enhancer that mediates the late phase of Hoxa3 expression through a conserved auto/cross-regulatory loop. This block of similarity is also present in the human and horn shark loci, and contains two bipartite Hox/Pbx-binding sites that are necessary for its in vivo activity in the hindbrain. These HOX/PBC sites are positioned near a conserved kreisler-binding site (KrA) that is involved in activating early expression in r5 and r6, but their activity is independent of kreisler. This work demonstrates that separate elements are involved in initiating and maintaining Hoxa3 expression during hindbrain segmentation, and that it is regulated in a manner different from Hoxb3 in later stages. Together, these findings add further strength to the emerging importance of positive auto- and cross-regulatory interactions between Hox genes as a general mechanism for maintaining their correct spatial patterns in the vertebrate nervous system.

Gene loss and gain in the evolution of the vertebrates

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 155-161
Author(s):  
Frank H. Ruddle ◽  
Kevin L. Bentley ◽  
Michael T. Murtha ◽  
Neil Risch
Keyword(s):  
Hox Genes ◽  
Gene Loss ◽  
Biological Function ◽  
Hox Gene ◽  
Step Process ◽  
Gene Expansion ◽  
Multiple Clusters ◽  
Adaptive Role ◽  
Hox Clusters

Homeobox cluster genes (Hox genes) are highly conserved and can be usefully employed to study phyletic relationships and the process of evolution itself. A phylogenetic survey of Hox genes shows an increase in gene number in some more recently evolved forms, particularly in vertebrates. The gene increase has occurred through a two-step process involving first, gene expansion to form a cluster, and second, cluster duplication to form multiple clusters. We also describe data that suggests that non-Hox genes may be preferrentially associated with the Hox clusters and raise the possibility that this association may have an adaptive biological function. Hox gene loss may also play a role in evolution. Hox gene loss is well substantiated in the vertebrates, and we identify additional possible instances of gene loss in the echinoderms and urochordates based on PCR surveys. We point out the possible adaptive role of gene loss in evolution, and urge the extension of gene mapping studies to relevant species as a means of its substantiation.

Analysis of cDNAs of the proto-oncogene c-src: heterogeneity in 5' exons and possible mechanism for the genesis of the 3' end of v-src

1991 ◽  
Vol 11 (8) ◽  
pp. 4165-4176
Author(s):  
T Dorai ◽  
J B Levy ◽  
L Kang ◽  
J S Brugge ◽  
L H Wang
Keyword(s):  
Cdna Library ◽  
Chicken Embryo ◽  
Termination Codon ◽  
Cdna Clones ◽  
Rnase Protection ◽  
Exon 2 ◽  
Brain Cdna Library ◽  
Exon 1 ◽  
Polymerase Chain

To further characterize the gene structure of the proto-oncogene c-src and the mechanism for the genesis of the v-src sequence in Rous sarcoma virus, we have analyzed genomic and cDNA copies of the chicken c-src gene. From a cDNA library of chicken embryo fibroblasts, we isolated and sequenced several overlapping cDNA clones covering the full length of the 4-kb c-src mRNA. The cDNA sequence contains a 1.84-kb sequence downstream from the 1.6-kb pp60c-src coding region. An open reading frame of 217 amino acids, called sdr (src downstream region), was found 105 nucleotides from the termination codon for pp60c-src. Within the 3' noncoding region, a 39-bp sequence corresponding to the 3' end of the RSV v-src was detected 660 bases downstream of the pp60c-src termination codon. The presence of this sequence in the c-src mRNA exon supports a model involving an RNA intermediate during transduction of the c-src sequence. The 5' region of the c-src cDNA was determined by analyzing several cDNA clones generated by conventional cloning methods and by polymerase chain reaction. Sequences of these chicken embryo fibroblast clones plus two c-src cDNA clones isolated from a brain cDNA library show that there is considerable heterogeneity in sequences upstream from the c-src coding sequence. Within this region, which contains at least 300 nucleotides upstream of the translational initiation site in exon 2, there exist at least two exons in each cDNA which fall into five cDNA classes. Four unique 5' exon sequences, designated exons UE1, UE2, UEX, and UEY, were observed. All of them are spliced to the previously characterized c-src exons 1 and 2 with the exception of type 2 cDNA. In type 2, the exon 1 is spliced to a novel downstream exon, designated exon 1a, which maps in the region of the c-src DNA defined previously as intron 1. Exon UE1 is rich in G+C content and is mapped at 7.8 kb upstream from exon 1. This exon is also present in the two cDNA clones from the brain cDNA library. Exon UE2 is located at 8.5 kb upstream from exon 1. The precise locations of exons UEX and UEY have not been determined, but both are more than 12 kb upstream from exon 1. The existence and exon arrangements of these 5' cDNAs were further confirmed by RNase protection assays and polymerase chain reactions using specific primers. Our findings indicate that the heterogeneity in the 5' sequences of the c-src mRNAs results from differential splicing and perhaps use of distinct initiation sites. All of these RNAs have the potential of coding for pp60c-src, since their 5' exons are all eventually joined to exon 2.

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