Alternatively polyadenylated calpastatin transcripts in bovine muscles / Transcriptos alternativamente poliadenilados de calpastatina en músculos de bovino

Calpastatin activity has a key role in the tenderization process that occurs during postmortem storage of meat under refrigerated conditioning. The regulation of calpastatin (CAST) expression is highly complex, the gene has four putative promoters and at least three different polyadenylation sites, and it is also alternatively spliced. We investigated the presence of alternative polyadenylation (APA) isoforms of CAST transcripts in three muscles (infraspinatus, triceps brachii and semitendinosus) of two bovine breeds (Angus and Brahman). The 3´ RACE-PCR was used to specifically amplify the different APA sites. The amplified fragments were cloned and sequenced. Sequencing confirmed the existence of three expected polyadenylation sites corresponding to short, medium and long polyadenylated transcripts. Also, transcripts with a novel APA site were found in the three muscles of both breeds. Because the same APAs isoforms were found between muscles and breeds, we could hypothesize a possible contribution to the relative abundance of different isoforms, probably in coordination with promoter preference and alternative splicing. This knowledge would be useful in the design of future experiments to analyze differential expression of CAST isoforms and their contribution to the definition of beef tenderness.

La actividad de la calpastatina tiene un rol clave en el proceso de tiernización postmortem de la carne durante su almacenamiento refrigerado. La regulación de la expresión de calpastatina (CAST) es altamente compleja; el gen tiene cuatro potenciales promotores, diferentes sitios de poliadenilación de transcriptos y también splicing alternativo. En este trabajo se investiga la presencia de isoformas de transcriptos de CAST alternativamente poliadenilados (APA) en tres músculos (infraspinatus, triceps brachii y semitendinosus) de dos razas bovinas (Angus y Brahman). Se utilizó la técnica de 3´ RACE-PCR para amplificar específicamente los diferentes sitios APA. Los fragmentos amplificados fueron clonados y secuenciados. La secuenciación confirmó la existencia de tres sitios de poliadenilación conocidos. Un nuevo sitio APA fue identificado en transcriptos de los tres músculos y en ambas razas. Dado que cualitativamente no hubo variación en la presencia de isoformas definidas por APA entre músculos y razas de terneza contrastante, podría hipotetizarse una posible contribución a la abundancia relativa de distintas isoformas, probablemente en forma coordinada con la elección de promotores y el splicing alternativo. Este nuevo conocimiento podría ser de utilidad para el diseño de experimentos de análisis de expresión diferencial de isoformas de calpastatina, para ponderar la contribución de las mismas a las variaciones en terneza de la carne.

mTOR-coordinated Post-Transcriptional Gene Regulations: from Fundamental to Pathogenic Insights

Post-transcriptional regulations of mRNA transcripts such as alternative splicing and alternative polyadenylation can affect the expression of genes without changing the transcript levels. Recent studies have demonstrated that these post-transcriptional events can have significant physiological impacts on various biological systems and play important roles in the pathogenesis of a number of diseases, including cancers. Nevertheless, how cellular signaling pathways control these post-transcriptional processes in cells are not very well explored in the field yet. The mammalian target of rapamycin complex 1 (mTORC1) pathway plays a key role in sensing cellular nutrient and energy status and regulating the proliferation and growth of cells by controlling various anabolic and catabolic processes. Dysregulation of mTORC1 pathway can tip the metabolic balance of cells and is associated with a number of pathological conditions, including various types of cancers, diabetes, and cardiovascular diseases. Numerous reports have shown that mTORC1 controls its downstream pathways through translational and/or transcriptional regulation of the expression of key downstream effectors. And, recent studies have also shown that mTORC1 can control downstream pathways via post-transcriptional regulations. In this review, we will discuss the roles of post-transcriptional processes in gene expression regulations and how mTORC1-mediated post-transcriptional regulations contribute to cellular physiological changes. We highlight post-transcriptional regulation as an additional layer of gene expression control by mTORC1 to steer cellular biology. These emphasize the importance of studying post-transcriptional events in transcriptome datasets for gaining a fuller understanding of gene expression regulations in the biological systems of interest.

Alternative Polyadenylation in Human Diseases

Varying length of messenger RNA (mRNA) 3′-untranslated region is generated by alternating the usage of polyadenylation sites during pre-mRNA processing. It is prevalent through all eukaryotes and has emerged as a key mechanism for controlling gene expression. Alternative polyadenylation (APA) plays an important role for cell growth, proliferation, and differentiation. In this review, we discuss the functions of APA related with various physiological conditions including cellular metabolism, mRNA processing, and protein diversity in a variety of disease models. We also discuss the molecular mechanisms underlying APA regulation, such as variations in the concentration of mRNA processing factors and RNA-binding proteins, as well as global transcriptome changes under cellular signaling pathway.

Biological functions of alternative polyadenylation / 军事医学

Alternative polyadenylation ( APA) is a widespread phenomenon and an important layer of gene regulation . APA contributes to the complexity of the transcriptome by allowing a single gene to encode multiple mRNA isoforms that dif -fer either in their coding sequence or in their 3′untranslated regions (3′UTR).The length of the 3′UTR can affect the sta-bility, localization and efficiency of the messenger RNAs ( mRNAs) by altering binding sites of RNA binding proteins or mi-croRNAs(miRNAs).The polyadenylation process , mechanisms governing APA and biological consequences resulting from APA are only starting to be deciphered .Here, we review the research progress in APA .

Progress in the relation between cleavage and polyadenylation specific factor and tumor / 国际外科学杂志

For human solid tumors,the preferred treatment is surgery.However most patients with clinical diagnosis of tumor is already in advanced,and lost the chance of operation.Cleavage and polyadenylation specific factor is involved in mRNA 3' end cleavage and polyadenine (A) tail,and plays an important role in mRNA maturation and intracellular singal transduction.Under certain conditions,cleavage and polyademletion specific factor can lead to abnormal activation of cancer genes,and then cause tumors.Progress in the relation between cleavage and polyademletion specific factor and tumor was reviewed in the paper.

Neuronal RNA granule contains ApCPEB1, a novel cytoplasmic polyadenylation element binding protein, in Aplysia sensory neuron

The cytoplasmic polyadenylation element (CPE)-binding protein (CPEB) binds to CPE containing mRNAs on their 3' untranslated regions (3'UTRs). This RNA binding protein comes out many important tasks, especially in learning and memory, by modifying the translational efficiency of target mRNAs via poly (A) tailing. Overexpressed CPEB has been reported to induce the formation of stress granules (SGs), a sort of RNA granule in mammalian cell lines. RNA granule is considered to be a potentially important factor in learning and memory. However, there is no study about RNA granule in Aplysia. To examine whether an Aplysia CPEB, ApCPEB1, forms RNA granules, we overexpressed ApCPEB1-EGFP in Aplysia sensory neurons. Consistent with the localization of mammalian CPEB, overexpressed ApCPEB1 formed granular structures, and was colocalized with RNAs and another RNA binding protein, ApCPEB, showing that ApCPEB1 positive granules are RNA-protein complexes. In addition, ApCPEB1 has a high turnover rate in RNA granules which were mobile structures. Thus, our results indicate that overexpressed ApCPEB1 is incorporated into RNA granule which is a dynamic structure in Aplysia sensory neuron. We propose that ApCPEB1 granule might modulate translation, as other RNA granules do, and furthermore, influence memory.

Conservation of cis-Regulatory Element Controlling Timely Translation in the 3'-UTR of Selected Mammalian Maternal Transcripts

The earliest stages of mammalian embryogenesis are governed by the activity of maternally inherited transcripts and proteins. Cytoplasmic polyadenylation of selected maternal mRNA has been reported to be a major control mechanism of delayed translation during preimplantation embryogenesis in mice. The presence of cis-elements required for cytoplasmic polyadenylation (e.g., CPE) can serve as a useful tag in the screening of maternal genes partaking in key functions in the transcriptionally dormant egg and early embryo. However, due to its relative simplicity, UA-rich sequences satisfying the canonical rule of known CPE consensus sequences are often found in the 3'-UTR of maternal transcripts that do not actually undergo cytoplasmic polyadenylation. In this study, we developed a method to confirm the validity of candidate CPE sequences in a given gene by a multiplex comparison of 3'-UTR sequences between mammalian homologs. We found that genes undergoing cytoplasmic polyadenylation tend to create a conserved block around the CPE, while CPE-like sequences in the 3'-UTR of genes lacking cytoplasmic polyadenylation do not exhibit such conservation between species. Through this cross-species comparison, we also identified an alternative CPE in the 3'-UTR of tissue-type plasminogen activator (tPA), which is more likely to serve as a functional element. We suggest that verification of CPEs based on sequence conservation can provide a convenient tool for mass screening of factors governing the earliest processes of mammalian embryogenesis.