scholarly journals Annelids win again: the first evidence of Hox antisense transcription in Spiralia

2021 ◽  
Author(s):  
Elena L. Novikova ◽  
Nadezhda I. Bakalenko ◽  
Milana A. Kulakova
Keyword(s):  
Hox Genes ◽  
Expression Patterns ◽  
Antisense Transcription ◽  
Antisense Transcripts ◽  
Platynereis Dumerilii ◽  
Non Coding Rnas ◽  
And Control ◽  
First Time ◽  
Hox Clusters

AbstractTo date it is becoming more and more obvious that multiple non-coding RNAs, once considered to be transcriptional noise, play a huge role in gene regulation during animal ontogenesis. Hox genes are key regulators of embryonic development, growth and regeneration of all bilaterian animals. It was shown that mammalian Hox loci are transcribed in both directions and noncoding RNAs maintain and control the normal functioning of Hox clusters. We revealed antisense transcripts of most of Hox genes in two lophotrochozoans, errant annelids Alitta virens and Platynereis dumerilii. It is for the first time when non-coding RNAs associated with Hox genes are found in spiralian animals. All these asRNAs can be referred to as natural antisense transcripts (NATs). We analyzed the expression of all detected NATs using sense probes to their Hox mRNAs during larval and postlarval development and regeneration by whole mount in situ hybridization (WMISH). We managed to clone several asRNAs (Avi-antiHox4-1, Avi-antiHox4-2 and Avi-antiHox5) of these annelids and analyzed their expression patterns as well. Our data indicate variable and complicated interplay between sense and antisense Hox transcripts during development and growth of two annelids. The presence of Hox antisense transcription in the representatives of different bilaterian clades (mammals, myriapods and annelids) and similar expression relationships in sense-antisense pairs suggest that this can be the ancestral feature of Hox cluster regulation.

scholarly journals There and Back Again: Hox Clusters Use Both DNA Strands

2021 ◽  
Vol 9 (3) ◽  
pp. 28
Author(s):  
Elena L. Novikova ◽  
Milana A. Kulakova
Keyword(s):  
Hox Genes ◽  
Regulatory Peptides ◽  
Antisense Transcription ◽  
Dna Strands ◽  
Epigenetic Code ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
Cis And Trans ◽  
In Cis ◽  
Hox Clusters

Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.

scholarly journals An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters

Development ◽  
2021 ◽  
Vol 148 (11) ◽  
Author(s):  
Kazuya Yamada ◽  
Akiteru Maeno ◽  
Soh Araki ◽  
Morimichi Kikuchi ◽  
Masato Suzuki ◽  
...  
Keyword(s):  
Hox Genes ◽  
Main Body ◽  
Loss Of Function ◽  
Micro Computed Tomography ◽  
Genetic Studies ◽  
Hox Cluster ◽  
Species Specific ◽  
First Time ◽  
Hox Clusters ◽  
Tomography Scan

ABSTRACT Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.

scholarly journals Novel Bionanocellulose/κ-Carrageenan Composites for Tissue Engineering

2018 ◽  
Vol 8 (8) ◽  
pp. 1352 ◽  
Author(s):  
Izabela Cielecka ◽  
Marcin Szustak ◽  
Edyta Gendaszewska-Darmach ◽  
Halina Kalinowska ◽  
Małgorzata Ryngajłło ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Chondrogenic Differentiation ◽  
Expression Patterns ◽  
Swelling Properties ◽  
In Situ Method ◽  
Chondrogenic Phenotype ◽  
The Impact ◽  
First Time ◽  
Water Holding

In this work, novel bacterial cellulose/κ-carrageenan (BNC/κ-Car) composites, being potential scaffolds for tissue engineering (TE), and outperforming the two polymers when used as scaffolds separately, were for the first time obtained using an in situ method, based on the stationary culture of bacteria Komagateibacter xylinus E25. The composites were compared with native BNC in terms of the morphology of fibers, chemical composition, crystallinity, tensile and compression strength, water holding capacity, water retention ratio and swelling properties. Murine chondrogenic ATDC5 cells were applied to assess the utility of the BNC/κ-Car composites as potential scaffolds. The impact of the composites on the cells viability, chondrogenic differentiation, and expression patterns of Col1α1, Col2α1, Runx2, and Sox9, which are indicative of ATDC5 chondrogenic differentiation, was determined. None of the composites obtained in this study caused the chondrocyte hypertrophy. All of them supported the differentiation of ATDC5 cells to more chondrogenic phenotype.

scholarly journals Spatiotemporal characterization of periocular mesenchyme heterogeneity during anterior segment development

2019 ◽  
Author(s):  
Kristyn L. Van Der Meulen ◽  
Oliver Vöcking ◽  
Megan L. Weaver ◽  
Jakub K. Famulski
Keyword(s):  
Expression Patterns ◽  
Anterior Segment ◽  
Critical Event ◽  
Transgenic Zebrafish ◽  
Anterior Segment Dysgenesis ◽  
Heterogenous Population ◽  
First Time

ABSTRACTEstablishment of the ocular anterior segment (AS) is a critical event during development of the vertebrate visual system. Failure in this process leads to Anterior Segment Dysgenesis (ASD), which is characterized by congenital blindness and predisposition to glaucoma. The anterior segment is largely formed via a neural crest-derived population, the Periocular Mesenchyme (POM). In this study, we aimed to characterize POM behaviors and identities during zebrafish AS development. POM distributions and migratory dynamics were analyzed using transgenic zebrafish embryos (Tg[foxC1b:GFP], Tg[foxD3:GFP], Tg[pitx2:GFP], Tg[lmx1b.1:GFP], and Tg[sox10:GFP] throughout the course of early AS development (24-72hpf). In vivo imaging analysis revealed unique AS distribution and migratory behavior among the reporter lines, suggesting AS mesenchyme (ASM) is a heterogenous population. This was confirmed using double in situ hybridization. Furthermore, we generated ASM transcriptomic profiles from our reporter lines and using a four-way comparison analysis uncovered unique ASM subpopulation expression patterns. Taken together, our data reveal for the first time that AS-associated POM is not homogeneous but rather comprised of several unique subpopulations identifiable by their distributions, behaviors, and transcriptomic profiles.

Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk

Development ◽  
1998 ◽  
Vol 125 (3) ◽  
pp. 407-420 ◽  
Author(s):  
V.E. Prince ◽  
L. Joly ◽  
M. Ekker ◽  
R.K. Ho
Keyword(s):  
Hox Genes ◽  
Genomic Organization ◽  
Expression Patterns ◽  
Regional Identity ◽  
Hoxa Cluster ◽  
Hox Cluster ◽  
Sequence Homologies ◽  
Race Pcr ◽  
Linkage Relationships ◽  
Hox Clusters

The Hox genes are implicated in conferring regional identity to the anteroposterior axis of the developing embryo. We have characterized the organization and expression of hox genes in the teleost zebrafish (Danio rerio), and compared our findings with those made for the tetrapod vertebrates. We have isolated 32 zebrafish hox genes, primarily via 3′RACE-PCR, and analyzed their linkage relationships using somatic cell hybrids. We find that in comparison to the tetrapods, zebrafish has several additional hox genes, both within and beyond the expected 4 hox clusters (A-D). For example, we have isolated a member of hox paralogue group 8 lying on the hoxa cluster, and a member of hox paralogue group 10 lying on the b cluster, no equivalent genes have been reported for mouse or human. Beyond the 4 clusters (A-D) we have isolated a further 3 hox genes (the hoxx and y genes), which according to their sequence homologies lie in paralogue groups 4, 6, and 9. The hoxx4 and hoxx9 genes occur on the same set of hybrid chromosomes, hinting at the possibility of an additional hox cluster for the zebrafish. Similar to their tetrapod counterparts, zebrafish hox genes (including those with no direct tetrapod equivalent) demonstrate colinear expression along the anteroposterior (AP) axis of the embryo. However, in comparison to the tetrapods, anterior hox expression limits are compacted over a short AP region; some members of adjacent paralogue groups have equivalent limits. It has been proposed that during vertebrate evolution, the anterior limits of Hox gene expression have become dispersed along the AP axis allowing the genes to take on novel patterning roles and thus leading to increased axial complexity. In the teleost zebrafish, axial organization is relatively simple in comparison to that of the tetrapod vertebrates; this may be reflected by the less dispersed expression domains of the zebrafish hox genes.

Expression Patterns of RNAs for Amelin and Amelogenin in Developing Rat Molars and Incisors

1996 ◽  
Vol 10 (2) ◽  
pp. 195-200 ◽  
Author(s):  
C.D. Fong ◽  
L. Hammarström ◽  
C. Lundmark ◽  
T. Wurtz ◽  
I. Slaby
Keyword(s):  
In Situ Hybridization ◽  
Expression Patterns ◽  
Paraffin Sections ◽  
Hybridization Procedure ◽  
Whole Mount ◽  
First Time ◽  
Developing Rat ◽  
Rat Molars ◽  
Oral Epithelia

We have recently identified a novel RNA sequence in ameloblasts, coding for amelin (Cerny et al., 1996). In the present paper, its expression has been compared with that of amelogenin in developing incisors and molars of rats, by means of in situ hybridization of paraffin sections. The RNAs for both amelin and amelogenin were highly expressed in secretory ameloblasts. The expression of RNA for amelogenin gradually decreased in the post-secretory ameloblasts. In contrast, the RNA expression for amelin remained high in post-secretory ameloblasts up to the stage of fusion between dental and oral epithelia at the time of tooth eruption. We suggest that amelin might be involved in the mineralization of enamel or in the attachment of ameloblasts to the enamel surface. The whole-mount in situ hybridization procedure is described for the first time in dental research. It proved to be a useful method and confirmed the results of the conventional in situ hybridization.

scholarly journals Lack of association between Epstein–Barr virus and mammary tumours in dogs

2018 ◽  
Vol 62 (3) ◽  
pp. 309-315
Author(s):  
Gustavo A. Roa López ◽  
Jhon Jairo Suárez ◽  
Paola Barato ◽  
Noel Verján García
Keyword(s):  
Breast Cancer ◽  
Mammary Gland ◽  
Epstein Barr Virus ◽  
Barr Virus ◽  
Mammary Tumours ◽  
Mammary Gland Cancer ◽  
Epstein Barr ◽  
And Control ◽  
First Time

AbstractIntroductionEpstein–Barr virus (EBV) is a γ-herpesvirus associated with various neoplasms in humans and is a probable aetiological agent in breast cancer; however, a causal relationship has not yet been established. Because of the epidemiological and clinicopathological similarities between breast cancer and canine mammary tumours, dogs have been proposed as a valid model for breast cancer.Material and MethodsA total of 47 canine mammary gland tumour tissues were processed by routine histopathological technique with haematoxylin-eosin staining and classified according to the type of neoplasm. DNA was extracted from paraffin-embedded tissues and the EBNA-1 gene and the BamHI-W region specific for EBV were evaluated by nested PCR.ResultsThe histopathological evaluation revealed 2 benign neoplasms, and many carcinomas: 2 in situ, 9 simple, 3 solid, 10 complex, and 21 mixed. One sample was positive for the EBNA-1 gene, while all were negative for the BamHI-W region.ConclusionNo association was found between EBV and mammary tumours in dogs. However, here we report for the first time the presence of an EBV gene sequence in a canine mammary tumour. It is likely that detection of EBV might be affected by the quality and quantity of DNA extracted from paraffin-embedded tissues. Additional studies are necessary to establish any association of EBV with mammary gland cancer in humans and in dogs, which could eventually lead to better public health prevention and control.

scholarly journals Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

2016 ◽  
Author(s):  
Sabrina M. Schiemann ◽  
José M. Martín-Durán ◽  
Aina Børve ◽  
Bruno C. Vellutini ◽  
Yale J. Passamaneck ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Molecular Basis ◽  
Hox Genes ◽  
Expression Data ◽  
Specific Expression ◽  
Spatial Expression ◽  
Morphological Novelties ◽  
Hox Clusters

AbstractTemporal collinearity is often regarded as the force preserving Hox clusters in vertebrate genomes. Studies that combine genomic and gene expression data in invertebrates would allow generalizing this observation across all animals, but are scarce, particularly within Lophotrochozoa (e.g., snails and segmented worms). Here, we use two brachiopod species –Terebratalia transversa, Novocrania anomala– to characterize the complement, cluster and expression of their Hox genes. T. transversa has an ordered, split cluster with ten genes (lab, pb, Hox3, dfd, scr, lox5, antp, lox4, post2, post1), while N. anomala has nine (missing post1). Our in situ hybridization, qPCR and stage specific transcriptomic analyses show that brachiopod Hox genes are neither strictly temporally nor spatially collinear; only pb (in T. transversa), Hox3 and dfd (in both brachiopods) show staggered mesodermal expression. The spatial expression of the Hox genes in both brachiopod species correlates with their morphology and demonstrates cooption of Hox genes in the chaetae and shell fields, two major lophotrochozoan morphological novelties. The shared and specific expression of a subset of Hox genes, Arx and Zic orthologs in chaetae and shell-fields between brachiopods, mollusks, and annelids supports the deep conservation of the molecular basis forming these lophotrochozoan hallmarks. Our findings challenge that collinearity alone preserves lophotrochozoan Hox clusters, indicating that additional genomic traits need to be considered in understanding Hox evolution.

Hoxa 11 structure, extensive antisense transcription, and function in male and female fertility

Development ◽  
1995 ◽  
Vol 121 (5) ◽  
pp. 1373-1385 ◽  
Author(s):  
H.M. Hsieh-Li ◽  
D.P. Witte ◽  
M. Weinstein ◽  
W. Branford ◽  
H. Li ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Homeobox Gene ◽  
Antisense Transcription ◽  
Developmental Expression ◽  
Female Sterility ◽  
Antisense Strand ◽  
Antisense Transcripts ◽  
Male And Female ◽  
Reading Frame ◽  
And Function

Hoxa 11 is a murine Abdominal-B-type homeobox gene. The structure of this gene is presented, including genomic and cDNA sequence. The cDNA includes the complete open reading frame and based on primer extension results is near full length. Surprisingly, the antisense strand of Hoxa 11 was found to be transcribed. Moreover, these antisense transcripts were processed and polyadenylated. The developmental expression patterns for both sense and antisense transcripts were examined using serial section and whole-mount in situ hybridizations. Hoxa 11 transcription patterns were defined in the limbs, kidney and stromal cells surrounding the Mullerian and Wolffian ducts. Of particular interest, in the developing limbs, the sense and antisense transcripts showed complementary expression patterns, with antisense RNAs increasing in abundance in regions where sense RNAs were diminishing in abundance. Furthermore, targeted mutation of Hoxa 11 is shown to result in both male and female sterility. The female mutants produce normal ova, which develop properly post-fertilization when transferred to wild-type surrogate mothers. The Hoxa 11 homozygous mutants are shown to provide a defective uterine environment. The mutant males exhibited a malformation of the vas deferens that resembles a partial homeotic transformation to an epididymis. In addition, the mutant testes fail to descend properly into the scrotum and, likely as a result, spermatogenesis is perturbed.

Homeodomain Expression in AML and T-ALL Cell Lines.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3369-3369
Author(s):  
Harry Drabkin ◽  
Sharvari Gadgil ◽  
Chan Zeng ◽  
Anna Baron ◽  
Olivier Bernard
Keyword(s):  
Gene Expression ◽  
Acute Leukemia ◽  
Cell Lines ◽  
Hox Genes ◽  
Expression Patterns ◽  
Disease Process ◽  
Hierarchical Cluster ◽  
Flt3 Expression ◽  
Low Incidence ◽  
Hox Clusters

Abstract HOX genes are frequent targets of chromosomal translocations and retroviral integrations in human and murine acute leukemia, often involving genes at the 5′-end of the HOX clusters. We previously reported that HOX expression patterns in AML were related to prognostic cytogenetic subsets. We also identified a distinct subset of patients with intermediate cytogenetics based on high levels of HOX and FLT3 expression, frequent FLT3 mutations and a low incidence of C/EBPa mutations. Certain cases of T-ALL also have rearrangements of homeodomain genes and some T-ALLs express limited myeloid markers. To further explore the spectrum of homeodomain gene expression, we developed qRT-PCR assays for nearly all clustered HOXA-D genes, selected homeodomain genes on chromosomes often altered in AML, and selected polycomb (Pc) genes, FLT3 and MLL. Altogether, 52 genes were analyzed in 32 AML and T-ALL cell lines. FLT3 expression was confined to a subset of AMLs. HOX11, HOX11L2 and NKX2.5 were expressed only in cases involving rearrangements of these genes. The Pc and MLL genes were uniformly expressed. Among HOX clusters, the frequency of gene expression was HOXA>B>C>D. Genes more highly expressed in the HOXC and D clusters were those at the 5′-ends (e.g., D13, C10). Marked or selective overexpression of individual genes suggests their possible involvement in the disease process, immortalization or differentiation. Examples include EN1 (SUPT1), D13 (MEGA1, B9 (PEER). A hierarchical cluster analysis based on homeodomain genes successfully identified subsets of related cell lines. Thus, the analysis of quantitative HOX expression may provide an important new tool to better understand the biology of acute leukemia.

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