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Transcriptome evidence provides insight into Hox gene regulating rolling behavior in oniscidea

ABSTRACT: Transcriptome evidence provides insight into Hox gene regulating rolling behavior in oniscidea

PROVIDER: PRJNA657520 | ENA |

REPOSITORIES: ENA

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Transcriptome evidence provides insight into Hox gene regulating rolling behavior in oniscidea

Project description:Behavior of rolling in oniscidea species had been reported as a sign to protect themselves to increase their survival rates, but the molecular mechanisms of rolling behaviors were still largely unknown. So we deeply characterized the molecular differences in rolling oniscidea samples and stretching oniscidea samples by transcriptome sequencing strategy (RNA-seq). Bulk RNA sequencing was performed with rolling and streching oniscidea samples. And our study suggests that Hox genes' expression levels could play an essential role in regulating neuron system development in oniscidea animals.

2021-01-26 | GSE156323 | GEO

RNA Seq analysis following RNAi perturbation of Hox genes in flatworm

Project description:Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis1. Emerging evidence for Hox gene expression and function in postnatally derived structures has fueled interest in their additional roles beyond embryogenesis2,3. We report novel functions for Hox genes in A/P directed adult tissue segmentation and transverse fission behavior underlying asexual reproduction in the planaria, Schmidtea mediterranea. Silencing of each of the 13 planarian Hox family members revealed 5 Hox genes required for asexual reproduction. Amongst these, silencing of hox3 genes resulted in supernumerary segments, while silencing of post2b eliminated segmentation altogether. The opposing roles of hox3 and post2b in segmentation are paralleled in the regulation of fission behavior. Silencing of hox3 increases the frequency of fission behavior initiation, while silencing of post2b eliminates fission behavior entirely. Furthermore, we identified a network of downstream effector genes mediating Hox gene regulation of asexual reproduction, thereby providing insight into their respective mechanisms of action. In summation, our study identifies roles for planarian Hox genes as mediators of adult tissue segmentation and behavior, as well as providing the first lines of evidence that Hox genes function post-embryonically to regulate asexual reproduction.

2021-08-13 | GSE159876 | GEO

Physiological and genome-wide expression analysis of cold-induced leaf rolling at the seedling stage in rice (Oryza sativa L.)

Project description:Leaf rolling and discoloration are two chilling injury symptoms that are widely adopted as indicators for evaluation of cold tolerance at the seedling stage in rice, respectively. However, their relationship has not been well investigated, in particular the mechanism on how low temperature causes leaf rolling at a genome-wide level. In this study, a cold-tolerant japonica cultivar Lijiangxintuanheigu and a cold-sensitive indica cultivar Sanhuangzhan-2 were subjected to different low temperature treatments and physiological and genome-wide gene expression analysis were conducted. Our results showed that leaf rolling happened at temperatures lower than 11℃, but discoloration appeared at moderately low temperatures, such as 13℃. Chlorophyll contents of the two cultivars significantly decreased under 13℃, but didn’t change under 11℃. Contrastly, their relative water contents and the relative electrolyte leakages decreased significantly. Genome-wide gene expression profiling of LTH revealed that the calcium signaling related genes and the genes related to ABA degradation significantly changed under 11℃. Moreover, numerous genes in DREB, MYB, bZIP, NAC, Zin finger, bHLH, WRKY gene families were differently expressed. Furthermore, many aquaporin genes, the key genes in trehalose and starch synthesis were down-regulated under 11℃. These results suggest that the two chilling injury symptoms are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways, and subjected to regulation of multiple transcription regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress result in reduction of water potential in cells and consequently, leaf rolling.

2019-03-30 | GSE112547 | GEO

Transcription profiling of Drosophila embryos at stages 11 and 12 to identify genes downstream of Hox

Project description:Identification of Hox gene downstream genes at embryonic stages 11 and 12<br><br>Functional diversification of body parts is dependent on the formation of specialized structures along the various body axes. In animals, region-specific morphogenesis along the anterior-posterior axis is controlled by a group of conserved transcription factors encoded by the Hox genes. Although it has long been assumed that Hox proteins carry out their function by regulating distinct sets of downstream genes, only a small number of such genes have been found, with very few having direct roles in controlling cellular behavior. We have quantitatively identified hundreds of Hox downstream genes in Drosophila by microarray analysis, and validated many of them by in situ hybridizations on loss- and gain-of-function mutants. One important finding is that Hox proteins, despite their similar DNA binding properties in vitro, have highly specific effects on the transcriptome in vivo, as expression of many downstream genes responds primarily to a single Hox protein. In addition, a large fraction of downstream genes encodes realizator functions, which directly affect morphogenetic processes, such as orientation and rate of cell divisions, cell-cell adhesion and communication, cell shape and migration, or cell death. Focusing on these realizators, we provide a framework for the morphogenesis of the maxillary segment. Since the genomic organization of Hox genes and the interaction of Hox proteins with specific cofactors are conserved in vertebrates and invertebrates, and similar classes of downstream genes are regulated by Hox proteins across the metazoan phylogeny, our findings represent a first step towards a mechanistic understanding of morphological diversification within a species as well as between species.

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Flow-through rolling tank

Project description:A flow-through rolling tank allows to conduct experiments on particulate organic matter at near in-situ conditions.

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Mapping genomic binding sites of Drosophila Hox proteins and Hox cofactors, Extradenticle and Homothorax, in Kc167 cells with transient expression [ChIP-seq_Transient]

Project description:We have carried out a systematic analysis of the in vivo genomic binding profiles of all eight Drosophila Hox proteins using transient transfection in Kc167 cells to examine Hox protein targeting. In addition, we have examined Hox protein binding in cells transfected with both Hox and the cofactor, Homothorax. Provision of Homothorax also recruits the cofactor Extradenticle.

2019-05-15 | GSE122574 | GEO

Comparision of Psip1/p75 binding and Mll1 binding sites on Hox and non-Hox genes

Project description:Psip1/p75 binds to Hox genes and colocalizes with Mll1 and in Psip1 KO MEFs Mll1 occupancy is reduced over Hox genes Psip1/p75 ChIP using A300-848 abtibody (recognises p75 isoform of Psip1) and Mll1 ChIP from WT and Psip1 KO MEFs ChIP-chip

2014-06-27 | E-GEOD-49179 | biostudies-arrayexpress

The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior.

Project description: Not available

| S-EPMC6681833 | biostudies-literature

Mapping genomic binding sites of Drosophila Hox proteins, Hox cofactors Extradenticle and Homothorax, and the pioneer factor Glial cells missing in stable cell lines [ChIP-seq_Stable]

Project description:We have carried out analysis of the in vivo genomic binding profiles of Drosophila Hox proteins using stable cell lines to examine Hox protein targeting. We have also examined Hox protein binding in stable cell lines expressing both Hox and the cofactor, Homothorax. Provision of Homothorax also recruits the cofactor Extradenticle.In addition, we have examined Hox protein binding in stable cell lines expressing both Hox and the pioneer factor, Glial cells missing in the absence or presence of Homothorax.

2019-05-15 | GSE122573 | GEO

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