Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues

2007 ◽  
Vol 29 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Luiz L. Coutinho ◽  
Lakshmi K. Matukumalli ◽  
Tad S. Sonstegard ◽  
Curtis P. Van Tassell ◽  
Louis C. Gasbarre ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bovine Genome ◽  
Regulation Of Gene Expression ◽  
Comparative Sequence Analysis ◽  
Cdna Libraries ◽  
Bovine Embryo ◽  
Draft Sequence ◽  
Stem Loop ◽  
Embryonic Tissues ◽  
Mature Micrornas

MicroRNAs are small ∼22 nucleotide-long noncoding RNAs capable of controlling gene expression by inhibiting translation. Alignment of human microRNA stem-loop sequences (mir) against a recent draft sequence assembly of the bovine genome resulted in identification of 334 predicted bovine mir. We sequenced five tissue-specific cDNA libraries derived from the small RNA fractions of bovine embryo, thymus, small intestine, and lymph node to validate these predictions and identify new mir. This strategy combined with comparative sequence analysis identified 129 sequences that corresponded to mature microRNAs (miR). A total of 107 sequences aligned to known human mir, and 100 of these matched expressed miR. The other seven sequences represented novel miR expressed from the complementary strand of previously characterized human mir. The 22 sequences without matches displayed characteristic mir secondary structures when folded in silico, and 10 of these retained sequence conservation with other vertebrate species. Expression analysis based on sequence identity counts revealed that some miR were preferentially expressed in certain tissues, while bta-miR-26a and bta-miR-103 were prevalent in all tissues examined. These results support the premise that species differences in regulation of gene expression by miR occur primarily at the level of expression and processing.

scholarly journals EVOLUTION AND VARIATION OF RENIN GENES IN MICE

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 651-667
Author(s):  
Douglas P Dickinson ◽  
Kenneth W Gross ◽  
Nina Piccini ◽  
Carol M Wilson
Keyword(s):  
Gene Expression ◽  
Submandibular Gland ◽  
Regulation Of Gene Expression ◽  
Inbred Strains ◽  
Duplication Event ◽  
Comparative Sequence Analysis ◽  
Chromosome 1 ◽  
Gene Encoding ◽  
Prior Estimate ◽  
Low Levels

ABSTRACT Inbred strains of mice carry Ren-1, a gene encoding the thermostable Renin-1 isozyme. Ren-1 is expressed at relatively low levels in mouse submandibular gland and kidney. Some strains also carry Ren-2, a gene encoding the thermolabile Renin-2 isozyme. Ren-2 is expressed at high levels in the mouse submandibular gland and at very low levels, if at all, in the kidney. Ren-1 and Ren-2 are closely linked on mouse chromosome 1, show extensive homology in coding and noncoding regions and provide a model for studying the regulation of gene expression. An investigation of renin genes and enzymatic activity in wild-derived mice identified several restriction site polymorphisms as well as putative variants in renin gene expression and protein structure. The number of renin genes carried by different subpopulations of wild-derived mice is consistent with the occurrence of a gene duplication event prior to the divergence of M. spretus (2.75-5.5 million yr ago). This conclusion is in agreement with a prior estimate based upon comparative sequence analysis of Ren-1 and Ren-2 from inbred laboratory mice.

scholarly journals Antigene-block strategy: Effective regulation of gene expression by 2′,4′-BNA-modified TFOs with an additional stem-loop structure

2005 ◽  
Vol 49 (1) ◽  
pp. 335-336 ◽  
Author(s):  
Naoto Tsuda ◽  
Ayumi Matsumoto ◽  
Aya Ito ◽  
Tomomi Uneda ◽  
Atsuhiro Tanabe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure

scholarly journals Identification of a post-transcriptional regulatory element that responds to glucose in the African trypanosome

2018 ◽  
Author(s):  
Yijian Qiu ◽  
Vijay Shankar ◽  
Rooksana E. Noorai ◽  
Nelson Yeung ◽  
Sarah Grace McAlpine ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nutrient Availability ◽  
Regulatory Element ◽  
Regulation Of Gene Expression ◽  
Blood Stage ◽  
Stem Loop ◽  
Dynamic Regulation ◽  
African Trypanosome ◽  
Atp Production ◽  
Altered Glucose

ABSTRACTThe ability to adapt to varying nutrient availability in changing environments is critical for successful parasitism. The lifecycle stages of the African trypanosome, Trypanosoma brucei, that infect the host mammalian bloodstream utilize glucose exclusively for ATP production. The finding that trypanosomes also inhabit other tissues that frequently contain lower glucose concentrations suggests blood stage parasites may have to respond to a dynamic environment with changing nutrient availability in order to survive. However, little is known about how the parasites coordinate gene expression with nutrient availability. Through transcriptome analysis, we have found blood stage parasites deprived of glucose alter gene expression in a pattern similar to transcriptome changes triggered by other stresses. A surprisingly low concentration of glucose (<10 μM) was required to initiate the response. To further understand the dynamic regulation of gene expression that occurs in response to altered glucose availability in the environment, we have interrogated the 3’UTR of cytochrome c oxidase subunit VI, a known lifecycle stage regulated gene, and have identified a stem-loop structure that confers glucose-responsive regulation at the translational level.

scholarly journals The perplexities of ZC3H12A self-mRNA regulation

2016 ◽  
Vol 63 (3) ◽  
Author(s):  
Mateusz Wawro ◽  
Jakub Kochan ◽  
Aneta Kasza
Keyword(s):  
Gene Expression ◽  
Biological Activity ◽  
Transcriptional Regulation ◽  
Untranslated Region ◽  
Regulation Of Gene Expression ◽  
Loop Structure ◽  
Stem Loop ◽  
Mrna Regulation ◽  
Stem Loop Structure ◽  
Post Transcriptional Regulation

The mechanisms regulating transcripts turnover are key processes in the regulation of gene expression. The list of proteins involved in mRNAs degradation is still growing, however, the details of RNase-mRNAs interaction are not fully understood. ZC3H12A is a recently discovered inflammation-related RNase engaged in the control of proinflammatory cytokines transcripts turnover. ZC3H12A regulates also its own transcript half-live. We studied the details of this regulation. Our results confirm the importance of the 3’UTR in ZC3H12A-dependent ZC3H12A mRNA degradations. We compared mouse and human stem‑loop structures present in this region and discovered that human conserved stem-loop structure is not sufficient for ZC3H12A-dependent degradation. However, this structure is important for ZC3H12A mRNA post-transcriptional regulation. Our studies emphasize the importance of surroundings of the identified stem-loop structure for its biological activity. Removing of this region together with stem-loop structure greatly inhibits ZC3H12A regulation of the investigated 3’-untranslated region (3’UTR).

Next-Gen sequencing of the transcriptome of triticale

2011 ◽  
Vol 9 (2) ◽  
pp. 181-184 ◽  
Author(s):  
Y. Xu ◽  
C. Badea ◽  
F. Tran ◽  
M. Frick ◽  
D. Schneiderman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Animal Feed ◽  
Brachypodium Distachyon ◽  
Regulation Of Gene Expression ◽  
454 Sequencing ◽  
Intergeneric Hybrid ◽  
Cdna Libraries ◽  
Immature Seeds ◽  
Biomass Yields ◽  
Reference Genomes

Triticale possesses favourable agronomic attributes originating from both its wheat and rye progenitors, including high grain and biomass yields. Triticale, primarily used as animal feed in North America, is an excellent candidate for production of industrial bio-products. Little is known about the coordination of gene expression of rye and wheat genomes in this intergeneric hybrid, but significant DNA losses from the parental genomes have been reported. To clarify the regulation of gene expression in triticale, we carried out 454 sequencing of cDNAs obtained from root, leaf, stem and floral tissues in different lines of triticale and rye exhibiting different phenotypes and assembled reads into contigs. Related to the data assembly were the absence of reference genomes and the paucity of rye sequences in GenBank or other public databases. Consequently, we have sequenced cDNA libraries from roots, seedlings, leaves, floral tissues and immature seeds to facilitate the identification of triticale sequences originating from rye. To further characterize the wheat-derived cDNAs, we also developed a database close to 25,000 non-redundant full-length wheat coding sequence genes, based on existing databases and contigs that were verified against protein sequences from the grass genomes of Brachypodium distachyon, rice, sorghum and maize.

scholarly journals Coherent feedforward regulation of gene expression byCaulobacterσTand GsrN during hyperosmotic stress

2018 ◽  
Author(s):  
Matthew Z. Tien ◽  
Benjamin J. Stein ◽  
Sean Crosson
Keyword(s):  
Gene Expression ◽  
Protein Expression ◽  
Cell Survival ◽  
Caulobacter Crescentus ◽  
Regulation Of Gene Expression ◽  
Hyperosmotic Stress ◽  
Transcriptional Level ◽  
Stem Loop ◽  
General Stress ◽  
Gene Expression Control

AbstractGsrN is a conserved small RNA that is under transcriptional control of the general stress sigma factor, σT, and that functions as a post-transcriptional regulator ofCaulobacter crescentussurvival under multiple stress conditions. We have defined features of GsrN structure that determine survival under hyperosmotic stress, and have applied transcriptomic and proteomic methods to identify regulatory targets of GsrN under hyperosmotic conditions. The 5’ end of GsrN, which includes a conserved cytosine-rich stem loop structure, is necessary for cell survival after osmotic upshock. GsrN both activates and represses gene expression in this stress condition. Expression of an uncharacterized open reading frame predicted to encode a glycine-zipper protein,osrP, is strongly activated by GsrN. Our data support a model in which GsrN physically interacts withosrPmRNA through its 5’ C-rich stem loop to enhance OsrP protein expression. We conclude thatsigT,gsrN, andosrPform a coherent feedforward loop in which σTactivatesgsrNandosrPtranscription during stress, and GsrN activates OsrP protein expression at the post-transcriptional level. This study delineates transcriptional and post-transcriptional layers ofCaulobactergene expression control during hyperosmotic stress, uncovers a new regulatory target of GsrN, and defines a coherent feedforward motif in theCaulobacterGSR regulatory network.ImportanceBacteria inhabit diverse niches, and must adapt their physiology to constant environmental fluctuations. A major response to environmental perturbation is to change gene expression.Caulobacterand other alphaproteobacteria initiate a complex gene expression program known as the general stress response (GSR) under conditions including oxidative stress, osmotic stress, and nutrient limitation. The GSR enables cell survival in these environments. Understanding how bacteria survive stress requires that we dissect gene expression responses, such as the GSR, at the molecular level. This study is significant as it defines transcriptional and post-transcriptional layers of gene expression regulation in response to hyperosmotic stress. We further provide evidence that coherent feedforward motifs influence the system properties of theCaulobacterGSR pathway.

scholarly journals Regulation of gene expression in the bovine blastocyst by CSF2 is disrupted by CRISPR/Cas9-mediated deletion of CSF2RA

2021 ◽  
Author(s):  
Yao Xiao ◽  
Kyungjun Uh ◽  
Veronica M Negrón-Pérez ◽  
Hannah Haines ◽  
Kiho Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reproductive Tract ◽  
Preimplantation Embryo ◽  
Regulation Of Gene Expression ◽  
Transcript Abundance ◽  
Bovine Embryo ◽  
Modulate Function ◽  
Altered Expression ◽  
Stimulating Factor ◽  
Bovine Blastocyst

Abstract Colony stimulating factor 2 (CSF2) functions in the reproductive tract to modulate function of the preimplantation embryo. The β subunit of the CSF2 receptor (CSF2RB) is not expressed in the embryo and signal transduction is therefore different than for myeloid cells where the receptor is composed of α (CSF2RA) and β subunits. Here, we produced embryos in which exons 5 and 6 of CSF2RA were disrupted using the CRISPR/Cas 9 system to test whether CSF2RA signaling was essential for actions of CSF2 in the bovine embryo. Wildtype and CSF2RA knockout embryos were treated with 10 ng/mL CSF2 or vehicle at day 5 of development. Blastocysts were harvested at day 8 to determine transcript abundance of 90 genes by real time PCR. Responses in female blastocysts were examined separately from male blastocysts because actions of CSF2 are sex-dependent. For wildtype embryos, CSF2 altered expression of 10 genes in females and 20 in males. Only three genes were affected by CSF2 in a similar manner for both sexes. Disruption of CSF2RA prevented the effect of CSF2 on expression for 9 of 10 CSF2-regulated genes in females and 19 of 20 genes in males. Results confirm the importance of CSF2RA for regulation of gene expression by CSF2 in the blastocyst.

scholarly journals 2 IDENTIFICATION OF GENES INDUCED BY THE CONCEPTUS IN THE BOVINE ENDOMETRIUM DURING THE PRE-IMPLANTATION PERIOD

2006 ◽  
Vol 18 (2) ◽  
pp. 109
Author(s):  
C. Klein ◽  
S. Bauersachs ◽  
S. Ulbrich ◽  
H. Meyer ◽  
S. Schmidt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Cdna Array ◽  
Cdna Libraries ◽  
Type I ◽  
Rt Pcr ◽  
Maternal Communication ◽  
Array Hybridization ◽  
Implantation Period

Early embryonic development, implantation, and maintenance of a pregnancy are critically dependent on an intact embryo-maternal communication. So far, only few signals involved in this dialogue have been identified. In ruminants, interferon tau (IFN�) plays a key role in the process of maternal recognition of pregnancy by exhibiting antiluteolytic activity. Even though many experimental findings indicate a pivotal role of IFN� in the context of embryo-maternal communication in ruminants, a number of other systems may be involved. To identify genes induced in the bovine endometrium by the signaling of the embryo, a combination of subtracted cDNA libraries and cDNA array hybridization was applied. Monozygotic twin pairs (n = 5) were used as the biological model. Pregnancy was created in one twin by transferring two in vitro-produced embryos on Day 7 of the estrous cycle; the other twin received a sham embryo transfer. Pregnant and nonpregnant twins were slaughtered at Day 18; endometrial tissue samples were recovered and processed for transcriptome analysis as described (Bauersachs et al. 2005 J. Mol. Endocrinol. 34, 889-908). Screening of 4608 clones of two subtracted libraries revealed 90 different up-regulated genes and mRNAs, of which almost 50% are known to be stimulated by type I interferons. Among these interferon-stimulated genes, the ISG15 system is assumed to be of particular interest, and several components were studied in more detail using in situ hybridization. The pattern of mRNA expression suggests that modification of endometrial proteins through ISG15ylation plays a fundamental role during the pre-implantation period. A classification of the identified genes based on Gene Ontologies revealed the prevalence of genes involved in regulation of gene expression, cell communication, cell growth, cell differentiation, cell proliferation, and cell adhesion, and also the prevalence of genes with immune-related functions. These results underline the intense response of the endometrium to the presence of a conceptus, culminating in the preparation of the maternal environment for embryonic implantation. Further, for eleven selected genes the expression in the endometrium was quantified by the use of real-time RT-PCR. Overall, the results of quantitative RT-PCR and array hybridization correlated very well. To our knowledge this study provides the first holistic gene expression analysis of the bovine endometrium during the pre-implantation period. The results underline the importance of IFN� as an embryo-derived pregnancy recognition signal and depict the molecular mechanisms at the mRNA level underlying the intense embryo-maternal dialog taking place at Day 18 of gestation.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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