scholarly journals Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Daniel Andergassen ◽  
Christoph P Dotter ◽  
Daniel Wenzel ◽  
Verena Sigl ◽  
Philipp C Bammer ◽  
...  
Keyword(s):  
Developmental Stages ◽  
High Rate ◽  
Allelic Expression ◽  
Rna Seq ◽  
Mouse Development ◽  
Specific Expression ◽  
Tissue Specific ◽  
Specific Strain ◽  
Specific Regulation ◽  
Escape From X Inactivation

To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.

Calcitonin/calcitonin gene-related peptide transcription unit: tissue-specific expression involves selective use of alternative polyadenylation sites

1984 ◽  
Vol 4 (10) ◽  
pp. 2151-2160
Author(s):  
S G Amara ◽  
R M Evans ◽  
M G Rosenfeld
Keyword(s):  
Regulation Of Gene Expression ◽  
Alternative Polyadenylation ◽  
Calcitonin Gene Related Peptide ◽  
Transcription Unit ◽  
Specific Expression ◽  
Tissue Specific ◽  
Related Peptide ◽  
Calcitonin Gene ◽  
Polyadenylation Sites ◽  
Specific Regulation

Different 3' coding exons in the rat calcitonin gene are used to generate distinct mRNAs encoding either the hormone calcitonin in thyroidal C-cells or a new neuropeptide referred to as calcitonin gene-related peptide in neuronal tissue, indicating the RNA processing regulation is one strategy used in tissue-specific regulation of gene expression in the brain. Although the two mRNAs use the same transcriptional initiation site and have identical 5' terminal sequences, their 3' termini are distinct. The polyadenylation sites for calcitonin and calcitonin gene-related peptide mRNAs are located at the end of the exons 4 and 6, respectively. Termination of transcription after the calcitonin exon does not dictate the production of calcitonin mRNA, because transcription proceeds through both calcitonin and calcitonin gene-related peptide exons irrespective of which mRNA is ultimately produced. In isolated nuclei, both polyadenylation sites appear to be utilized; however, the proximal (calcitonin) site is preferentially used in nuclei from tissues producing calcitonin mRNA. These data suggest that the mechanism dictating production of each mRNA involves the selective use of alternative polyadenylation sites.

scholarly journals Developmental Expression of Mouse Erythrocyte Protein 4.2 mRNA: Evidence for Specific Expression in Erythroid Cells

Blood ◽  
1998 ◽  
Vol 91 (2) ◽  
pp. 695-705 ◽  
Author(s):  
Lingyun Zhu ◽  
Samir B. Kahwash ◽  
Long-Sheng Chang
Keyword(s):  
Mrna Expression ◽  
Fetal Liver ◽  
Late Gestation ◽  
Developmental Expression ◽  
Erythroid Cells ◽  
Mouse Development ◽  
Specific Expression ◽  
Protein 4.2 ◽  
Specific Regulation ◽  
In Erythroid Cells

Abstract Erythrocyte protein 4.2 (P4.2) is an important component of the erythrocyte membrane skeletal network with an undefined biologic function. Presently, very little is known about the expression of the P4.2 gene during mouse embryonic development and in adult animals. By using the Northern blot and in situ hybridization techniques, we have examined the spatial and temporal expression of the P4.2 gene during mouse development. We show that expression of the mouse P4.2 gene is temporally regulated during embryogenesis and that the P4.2 mRNA expression pattern coincides with the timing of erythropoietic activity in hematopoietic organs. P4.2 transcripts are first detected in embryos on day 7.5 of gestation and are localized exclusively in primitive erythroid cells of yolk sac origin. These erythroid cells remain to be the only source for P4.2 expression until the switch of the hematopoietic producing site to fetal liver. In mid- and late-gestation periods, P4.2 mRNA expression is restricted to the erythroid cells in fetal liver and to circulating erythrocytes. Around and after birth, the site for P4.2 expression is switched from liver to spleen and bone marrow, and P4.2 transcripts are only detected in cells of the erythroid lineage. These results provide the evidence for specific P4.2 expression in erythroid cells. In addition, the timing and pattern of expression of the P4.2 gene suggest the specific regulation of the P4.2 gene.

Stage and tissue-specific expression of fosB during mouse development

1991 ◽  
Vol 46 (1) ◽  
pp. 43-49 ◽  
Author(s):  
Brunhild Redemann-Fibi ◽  
Marcus Schuermann ◽  
Rolf Miiller
Keyword(s):  
Mouse Development ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Tissue-specific regulation of the expression of rat kallikrein gene family members by thyroid hormone

1990 ◽  
Vol 267 (3) ◽  
pp. 745-750 ◽  
Author(s):  
J A Clements ◽  
B A Matheson ◽  
J E Funder
Keyword(s):  
Gene Family ◽  
Hormonal Regulation ◽  
Female Rats ◽  
Hormonal Status ◽  
Mrna Levels ◽  
Specific Expression ◽  
Male And Female ◽  
Tissue Specific ◽  
Male And Female Rats ◽  
Specific Regulation

We have altered the thyroid hormonal status of both male and female rats and examined the expression of six functional members of the rat kallikrein gene family (PS, S1, S2, S3, K1 and P1) in the submandibular gland (SMG), kidney, prostate, testis and anterior pituitary gland (AP) of these animals. On Northern-blot analysis with gene-specific oligonucleotide probes, the steady-state mRNA levels of S1, S2, S3, K1 and P1 were all dramatically altered in the SMG of male and female rats treated with propylthiouracil (PTU; 100 mg/litre of drinking water) or thyroxine (T4; 10 micrograms/100 mg body wt.) for 3 weeks. The SMG mRNA levels of these five genes were all lowered (30-90%) in hypothyroid (PTU-treated) male and female rats and elevated (1.4-4-fold, male; 1.5-11-fold, female) in the hyperthyroid (T4-treated) and PTU/T4-treated animals. In contrast, PS (true kallikrein) mRNA levels in the male or female SMG or kidney were essentially unchanged. K1 mRNA levels in the kidney were considerably less responsive to thyroid status than those in the SMG. Changes in S3 and P1 mRNA levels in the prostate were also variable, but essentially unaffected by these treatments. AP PS mRNA levels were also unaffected by changes in thyroid-hormonal status, as were levels of a novel P1-like mRNA in the testis. In summary, these studies demonstrate that the same kallikrein gene family member(s) may be differentially regulated by thyroid hormones in the rat SMG, kidney, prostate and pituitary, and thus further extend the concept of tissue-specific expression and hormonal regulation of the kallikrein gene family in the rat.

scholarly journals Structure-specific regulation of nutrient absorption, metabolism and transfer in arbuscular mycorrhizal fungi

2018 ◽  
Author(s):  
Hiromu Kameoka ◽  
Taro Maeda ◽  
Nao Okuma ◽  
Masayoshi Kawaguchi
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Nutrient Absorption ◽  
Rna Seq ◽  
Specific Expression ◽  
Symbiotic Relationships ◽  
Specific Regulation ◽  
Fungal Nutrition

AbstractArbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with most land plants, mainly for the purpose of nutrient exchange. Many studies have revealed the regulation of absorption, metabolism, and transfer of nutrients in AMF and the genes involved in these processes. However, the spatial regulation of the genes among the structures comprising each developmental stage are not well understood. Here, we demonstrate the structure-specific transcriptome of the model AMF species, Rhizophagus irregularis. We performed an ultra-low input RNA-seq analysis, SMART-seq2, comparing five extraradical structures, germ tubes, runner hyphae, branched absorbing structures, immature spores, and mature spores. In addition, we reanalyzed the recently reported RNA-seq data comparing intraradical hyphae and arbuscules. Our analyses captured the distinct features of each structure and revealed the structure-specific expression patterns of genes related to absorption, metabolism, and transfer of nutrients. Of note, the transcriptional profiles suggest the distinct functions of branched absorbing structures in nutrient absorption. These findings provide a comprehensive dataset to advance our understanding of the transcriptional dynamics of fungal nutrition in this symbiotic system.

scholarly journals Cell-specific expression buffering promotes cell survival and cancer robustness

2021 ◽  
Author(s):  
Hao-Kuen Lin ◽  
Jen-Hao Cheng ◽  
Chia-Chou Wu ◽  
Feng-Shu Hsieh ◽  
Carolyn A Dunlap ◽  
...  
Keyword(s):  
Cell Survival ◽  
Rna Seq ◽  
Specific Expression ◽  
Tissue Specific ◽  
Gene Pairs ◽  
Genome Wide ◽  
A Cell ◽  
Physiological Homeostasis ◽  
Multicellular Organisms ◽  
Score Index

Functional buffering ensures biological robustness critical for cell survival and physiological homeostasis in response to environmental challenges. However, in multicellular organisms, the mechanism underlying cell- and tissue-specific buffering and its implications for cancer development remain elusive. Here, we propose a Cell-specific Expression-BUffering (CEBU) mechanism, whereby a gene's function is buffered by cell-specific expression of a buffering gene, to describe functional buffering in humans. The likelihood of CEBU between gene pairs is quantified using a C-score index. By computing C-scores using genome-wide CRISPR screens and transcriptomic RNA-seq of 684 human cell lines, we report that C-score-identified putative buffering gene pairs are enriched for members of the same pathway, protein complex and duplicated gene family. Furthermore, these buffering gene pairs contribute to cell-specific genetic interactions and are indicative of tissue-specific robustness. C-score derived buffering capacities can help predict patient survival in multiple cancers. Our results reveal CEBU as a critical mechanism of functional buffering contributing to cell survival and cancer robustness in humans.

scholarly journals Genome-wide and expression analysis of B-box gene family in pepper

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jing Ma ◽  
Jia-xi Dai ◽  
Xiao-wei Liu ◽  
Duo Lin
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transient Expression Assay ◽  
Specific Expression ◽  
Tissue Specific ◽  
Duplication Events ◽  
Onion Inner Epidermis

Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.

scholarly journals scBASE: A Bayesian mixture model for the analysis of allelic expression in single cells

2018 ◽  
Author(s):  
Kwangbom Choi ◽  
Narayanan Raghupathy ◽  
Gary A. Churchill
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Allelic Expression ◽  
Biological Variability ◽  
Rna Seq ◽  
Dynamic Features ◽  
Specific Expression ◽  
Bayesian Mixture Model ◽  
Bayesian Mixture ◽  
Allele Specific

Allele-specific expression (ASE) at single-cell resolution is a critical tool for understanding the stochastic and dynamic features of gene expression. However, low read coverage and high biological variability present challenges for analyzing ASE. We propose a new method for ASE analysis from single cell RNA-Seq data that accurately classifies allelic expression states and improves estimation of allelic proportions by pooling information across cells.

scholarly journals Stage and tissue-specific expression of the alcohol dehydrogenase 1 (Adh-1) gene during mouse development

1994 ◽  
Vol 199 (3) ◽  
pp. 199-213 ◽  
Author(s):  
Jean-Luc Vonesch ◽  
Harikrishna Nakshatri ◽  
Murielle Philippe ◽  
Pierre Chambon ◽  
Pascal Dollé
Keyword(s):  
Alcohol Dehydrogenase ◽  
Mouse Development ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Alcohol Dehydrogenase 1

scholarly journals Tissue-Specific Expression of a Rat Renin Transcript Lacking the Coding Sequence for the Prefragment and Its Stimulation by Myocardial Infarction*

Endocrinology ◽  
2000 ◽  
Vol 141 (8) ◽  
pp. 2963-2970 ◽  
Author(s):  
Susanne Clausmeyer ◽  
Alexander Reinecke ◽  
Raphaela Farrenkopf ◽  
Thomas Unger ◽  
Jörg Peters
Keyword(s):  
Myocardial Infarction ◽  
Adrenal Gland ◽  
Messenger Rna ◽  
Secretory Pathway ◽  
Alternative Transcript ◽  
Regulation Of Expression ◽  
Specific Expression ◽  
Tissue Specific ◽  
Renin Angiotensin ◽  
Specific Regulation

An alternative transcript of the rat renin gene was recently characterized in the adrenal gland, in addition to the known messenger RNA (mRNA) coding for preprorenin. In the alternative transcript, exon 1 is replaced by exon 1A, a domain originating in intron 1. The reading frame of this mRNA, termed exon 1A-renin transcript, codes for a truncated prorenin that presumably remains intracellular, in contrast to preprorenin, which is targeted to the secretory pathway by its prefragment. We here demonstrate the tissue-specific regulation of expression of both transcripts by RT and PCR. In many tissues both transcripts are present, for example in the adrenal gland, spleen, liver, and hypothalamus. In some organs, however, only one of the renin mRNAs is found. In the kidney only the full-length mRNA coding for preprorenin is detected. In the heart exclusively the exon 1A-mRNA is expressed, but not the preprorenin transcript. After myocardial infarction, which is known to activate the intracardiac renin-angiotensin system, expression of exon 1A-renin mRNA in the left ventricle was stimulated about 4-fold, compared with that in sham-operated animals, whereas no mRNA corresponding to preprorenin was detectable. These findings may have implications for the current concepts of local extrarenal renin-angiotensin systems, as they provide the molecular basis for a possible intracellular function of renin and exclude a role for locally produced secretory renin in the heart.

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