scholarly journals Localization of RNA Pol II CTD (S5) and Transcriptome Analysis of Testis in Diploid and Tetraploid Hybrids of Red Crucian Carp (♀) × Common Carp (♂)

2021 ◽  
Vol 12 ◽  
Author(s):  
Yi Zhou ◽  
La Zhu ◽  
Yu Sun ◽  
Hui Zhang ◽  
Jiaojiao Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Common Carp ◽  
Active Sites ◽  
Crucian Carp ◽  
Rna Seq ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Gradual Process ◽  
Red Crucian Carp ◽  
Significant Difference

Polyploidy occurs naturally in fish; however, the appearance of these species is an occasional and gradual process, which makes it difficult to trace the changes in phenotypes, genotypes, and regulation of gene expression. The allotetraploid hybrids (4nAT) of red crucian carp (RCC; ♀) × common carp (CC; ♂) generated from interspecies crossing are a good model to investigate the initial changes after allopolyploidization. In the present study, we focused on the changes in the active sites of the testicular transcriptome of the allotetraploid by localization of RNA Pol II CTD YSPTSPS (phospho S5) using immunofluorescence and RNA-seq data via bioinformatic analysis. The results showed that there was no significant difference in signal counts of the RNA Pol II CTD (S5) between the different types of fish at the same stages, including RCC, CC, 2nF1, and 4nAT, which means that the number of transcriptionally active sites on germ cell chromosomes was not affected by the increase in chromosome number. Similarly, RNA-seq analysis indicated that in the levels of chromosomes and 10-kb regions in the genome, there were no significant changes in the highly active sites in RCC, 2nF1, and 4nAT. These findings suggest that at the beginning of tetraploid origin, the active transcriptome site of 4nAT in the testis was conserved in the regions of the genome compared to that in RCC and 2nF1. In conclusion, 4nAT shared a similar gene expression model in the regions of the genome with RCC and 2nF1 with significantly different expression levels.

scholarly journals Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Lihai Ye ◽  
Chun Zhang ◽  
Xiaojun Tang ◽  
Yiyi Chen ◽  
Shaojun Liu
Keyword(s):  
Common Carp ◽  
Crucian Carp ◽  
Red Crucian Carp

The formation of improved tetraploid population of red crucian carp × common carp hybrids by androgenesis

2007 ◽  
Vol 50 (6) ◽  
pp. 753-761 ◽  
Author(s):  
Wei Duan ◽  
QinBo Qin ◽  
Song Chen ◽  
ShaoJun Liu ◽  
Jing Wang ◽  
...  
Keyword(s):  
Common Carp ◽  
Crucian Carp ◽  
Tetraploid Population ◽  
Red Crucian Carp

scholarly journals In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

2019 ◽  
Author(s):  
Rodrigo G. Arzate-Mejía ◽  
Angel Josué Cerecedo-Castillo ◽  
Georgina Guerrero ◽  
Mayra Furlan-Magaril ◽  
Félix Recillas-Targa
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Topological Defects ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Domain Boundaries ◽  
Topologically Associated Domains ◽  
Genetic Sequences

AbstractThe molecular mechanisms responsible for Topologically Associated Domains (TADs) formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by Architectural Proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence on the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila.

scholarly journals Cohesin removal reprograms gene expression upon mitotic entry

2019 ◽  
Author(s):  
Carlos Perea-Resa ◽  
Leah Bury ◽  
Iain Cheeseman ◽  
Michael D. Blower
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Rna Polymerase Ii ◽  
Chromosome Segregation ◽  
List Type ◽  
Mitotic Chromosomes ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Mitotic Entry ◽  
Nascent Transcripts

SummaryEntering mitosis, the genome is restructured to facilitate chromosome segregation, accompanied by dramatic changes in gene expression. However, the mechanisms that underlie mitotic transcriptional regulation are unclear. In contrast to transcribed genes, centromere regions retain transcriptionally active RNA Polymerase II (RNAPII) in mitosis. Here, we demonstrate that chromatin-bound cohesin is sufficient to retain RNAPII at centromeres while WAPL-mediated removal of cohesin during prophase is required for RNAPII dissociation from chromosome arms. Failure to remove cohesin from chromosome arms results in a failure to release elongating RNAPII and nascent transcripts from mitotic chromosomes and dramatically alters gene expression. We propose that prophase cohesin removal is the key step in reprogramming gene expression as cells transition from G2 to mitosis, and is temporally coupled with chromosome condensation to coordinate chromosome segregation with changes in gene expression.HighlightsMitotic centromere transcription requires cohesinCohesin removal releases elongating RNA Pol II and nascent RNA from chromatinThe prophase pathway reprograms gene expression during mitosis

Evolutionary analysis of allotetraploid hybrids of red crucian carp × common carp, based on ISSR, AFLP molecular markers and cloning of cyclins genes

2009 ◽  
Vol 54 (16) ◽  
pp. 2849-2861 ◽  
Author(s):  
LiangGuo Liu ◽  
JinPeng Yan ◽  
ShaoJun Liu ◽  
Dong Liu ◽  
CuiPing You ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Common Carp ◽  
Crucian Carp ◽  
Evolutionary Analysis ◽  
Red Crucian Carp

scholarly journals RNA Polymerase I Transcribes Procyclin Genes and Variant Surface Glycoprotein Gene Expression Sites in Trypanosoma brucei

2003 ◽  
Vol 2 (3) ◽  
pp. 542-551 ◽  
Author(s):  
Arthur Günzl ◽  
Thomas Bruderer ◽  
Gabriele Laufer ◽  
Bernd Schimanski ◽  
Lan-Chun Tu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Trypanosoma Brucei ◽  
Protein C ◽  
Gene Promoter ◽  
Surface Glycoprotein ◽  
Variant Surface Glycoprotein ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Pol I

ABSTRACT In eukaryotes, RNA polymerase (pol) I exclusively transcribes the large rRNA gene unit (rDNA) and mRNA is synthesized by RNA pol II. The African trypanosome, Trypanosoma brucei, represents an exception to this rule. In this organism, transcription of genes encoding the variant surface glycoprotein (VSG) and the procyclins is resistant to α-amanitin, indicating that it is mediated by RNA pol I, while other protein-coding genes are transcribed by RNA pol II. To obtain firm proof for this concept, we generated a T. brucei cell line which exclusively expresses protein C epitope-tagged RNA pol I. Using an anti-protein C immunoaffinity matrix, we specifically depleted RNA pol I from transcriptionally active cell extracts. The depletion of RNA pol I impaired in vitro transcription initiated at the rDNA promoter, the GPEET procyclin gene promoter, and a VSG gene expression site promoter but did not affect transcription from the spliced leader (SL) RNA gene promoter. Fittingly, induction of RNA interference against the RNA pol I largest subunit in insect-form trypanosomes significantly reduced the relative transcriptional efficiency of rDNA, procyclin genes, and VSG expression sites in vivo whereas that of SL RNA, αβ-tubulin, and heat shock protein 70 genes was not affected. Our studies unequivocally show that T. brucei harbors a multifunctional RNA pol I which, in addition to transcribing rDNA, transcribes procyclin genes and VSG gene expression sites.

scholarly journals Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells

2013 ◽  
Vol 26 (1) ◽  
pp. 101-112 ◽  
Author(s):  
Tony D. Southall ◽  
Katrina S. Gold ◽  
Boris Egger ◽  
Catherine M. Davidson ◽  
Elizabeth E. Caygill ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Neural Stem Cells ◽  
Cell Isolation ◽  
Chromatin Binding ◽  
Cell Type ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Cell Type Specific

scholarly journals Sequential Entry of Components of Gene Expression Machinery into Daughter Nuclei

2003 ◽  
Vol 14 (3) ◽  
pp. 1043-1057 ◽  
Author(s):  
Kannanganattu V. Prasanth ◽  
Paula A. Sacco-Bubulya ◽  
Supriya G. Prasanth ◽  
David L. Spector
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Mrna Processing ◽  
Mrna Splicing ◽  
Splicing Factors ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
General Transcription Factors ◽  
Sequential Entry ◽  
Processing Factors

In eukaryotic cells, RNA polymerase II (RNA pol II) transcription and pre-mRNA processing are coordinated events. We have addressed how individual components of the transcription and pre-mRNA processing machinery are organized during mitosis and subsequently recruited into the newly formed daughter nuclei. Interestingly, localization studies of numerous RNA pol II transcription and pre-mRNA processing factors revealed a nonrandom and sequential entry of these factors into daughter nuclei after nuclear envelope/lamina formation. The initiation competent form of RNA pol II and general transcription factors appeared in the daughter nuclei simultaneously, but prior to pre-mRNA processing factors, whereas the elongation competent form of RNA pol II was detected even later. The differential entry of these factors rules out the possibility that they are transported as a unitary complex. Telophase nuclei were competent for transcription and pre-mRNA splicing concomitant with the initial entry of the respective factors. In addition, our results revealed a low turnover rate of transcription and pre-mRNA splicing factors during mitosis. We provide evidence to support a model in which the entry of the RNA pol II gene expression machinery into newly forming daughter nuclei is a staged and ordered process.

scholarly journals Characterization of the rat developmental liver transcriptome

2013 ◽  
Vol 45 (8) ◽  
pp. 301-311 ◽  
Author(s):  
Richard H. Chapple ◽  
Polyana C. Tizioto ◽  
Kevin D. Wells ◽  
Scott A. Givan ◽  
JaeWoo Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput Sequencing ◽  
Mitochondrial Gene ◽  
Probe Design ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Biologically Relevant ◽  
Gradual Process ◽  
Intergenic Regions ◽  
Sequencing Platforms

Gene regulation and transcriptome studies have been enabled by the development of RNA-Seq applications for high-throughput sequencing platforms. Next generation sequencing is remarkably efficient and avoids many issues inherent in hybridization-based microarray methodologies including the exon-specific dependence of probe design. Biologically relevant transcripts including messenger and regulatory RNAs may now be quantified and annotated regardless of whether they have previously been observed. We used RNA-Seq to investigate global patterns of gene expression in early developing rat liver. Liver samples from timed-pregnant Lewis rats were collected at six fetal and neonatal stages [embryonic day (E)14, E16, E18, E20, postnatal day (P)1, P7], transcripts were sequenced using an Illumina HiSeq 2000, and data analysis was performed with the Tuxedo software suite. Genes and isoforms differing in abundance were queried for enrichment within functionally related gene groups using the Functional Annotation Tool of the DAVID Bioinformatics Database. While hematopoietic gene expression is initiated by E14, hepatocyte maturation is a gradual process involving clusters of genes responsible for response to nutrients and enzymes responsible for glycolysis and fatty acid catabolism. Following birth, a large cluster of differentially abundant genes was enriched for mitochondrial gene expression and cholesterol synthesis indicating that by 1 wk of age, the liver is engaged in lipid sensing and bile production. Clustering results for differentially abundant genes and isoforms were similar with the greatest difference for the E14/E16 comparison. Finally, a bioinformatic approach was used to annotate 1,307 novel liver transcripts assembled from sequences that aligned to intergenic regions of the rat genome.

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