Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF-α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads. On average, 105 million clean reads were mapped and in total 6091 significantly differentially expressed genes (DEGs) were identified (p < 0.05). These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database (GSE95371). We report the use of RNA sequencing to find DEGs that are affected by different feeding regimes in the thymus.

Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection. We used Phred/Phrap computer programs for analysis of the raw EST and readable EST sequences were assembled with the CAP3 software. Putative functions of all unique sequences and statistical analysis were determined by Geneious software. Total 422 ESTs have over 80% similarity to known sequences of other organisms in NCBI classified by Panther database for the Gene Ontology (GO) category. By comparing gene expression profiles, we observed some putative genes that may be relative to reproductive performance or play important roles in milk synthesis and secretion. A total of 2414 ESTs have been deposited to the NCBI GenBank database (GW996847–GW999260). EST data in this study have provided a new source of information to functional genome studies of sheep.

Mammary gland tumor is the most common type of tumor in female dogs. Data on genes that are involved in tumorigenesis and mechanism of tumor development are insufficient. Comparative studies have been conducted in order to see if tumorigenesis studies in the dog could be a model for human mammary gland tumors. In this study, we constructed two different cDNA libraries from mammary tissue, which were collected from a normal mammary tissue of a healthy Terrier dog and a tumoral mammary tissue of a sick dog. A total 2304 colonies which are randomly picked out from the two libraries were sequenced for developing a dog mammary gland ESTs collection. Raw EST data were analyzed with Phred/Phrap programs and readable EST sequences were assembled with the CAP3 program. All of EST sequences were grouped into 45 contig and 2203 singletons. Putative functions of all unique sequences were designated by NCBI BLAST based on gene homology and annotated by BLAST2GO. The results of this study are a very valuable resource for functional genome studies of the dogs. Keywords: Terrier, Dog, Breast cancer, EST, cDNA library Terrier Köpeklerinin Normal ve Tümörlü Meme Bezi Dokusunda Eksprese Edilen Genlerin Birincil Analizi ÖzMeme bezi tümörü, dişi köpeklerde en sık rastlanan tümör türüdür. Tümör oluşumu ve tümör oluşum mekanizması ile ilgili genler hakkındaki veriler yetersizdir. Köpekteki tümörigenez çalışmalarının insan meme bezi tümörleri için bir model olabileceğini görmek için karşılaştırmalı çalışmalar yürütülmüştür. Bu çalışmada, sağlıklı bir Terrier köpeğinin normal meme dokusundan ve hasta bir köpekten tümörlü meme dokusundan toplanan iki farklı dokudan iki farklı cDNA kütüphanesi oluşturuldu. Bir köpek meme bezi EST kolleksiyonu geliştirmek için, iki kütüphaneden rastgele seçilen toplam 2304 koloni dizilendi. Ham EST verileri Phred/Phrap programları ile analiz edildi ve okunabilir EST dizileri CAP3 programı ile bir araya getirildi. Tüm EST dizileri 45 kontig ve 2203 singlet grubuna ayrıldı. Tüm benzersiz sekansların varsayımsal fonksiyonları, NCBI BLAST tarafından gen homolojisine dayalı olarak belirlendi ve BLAST2GO ile açıklandı. Bu çalışmanın sonuçları, köpeklerin fonksiyonel genom çalışmaları için çok değerli bir kaynaktır.

Dogs share a common environment with humans and knowledge of the specific dog breed diseases is very useful in developing a model for human cancer studies. ESTs represent part of the transcribed genome of an organism and are an important resource for identifying microsatellites. Simple Sequence Repeats (SSRs), or microsatellites, which contain repetitive DNA sequences, are among the most powerful genetic markers known. The development of EST-SSRs has become a fast, efficient, and low-cost option for genomic studies. In this study, to determine SSRs from EST libraryof mammary gland tissue of the Terrier dog that has 2304 ESTs; SSRIT and IMEx software, which have web-based versions and are easily accessible, were used. SSRIT finds motifs from 2 to 10 base lengths and adjusts the minimum number of repeats by eliminating single nucleotide motifs. IMEx finds perfect and imperfect microsatellites separately. It can find motifs of different lengths from 1 to 6 and the minimum number of repeats can be set. In addition, the appropriate primer for the desired SSR region can be designed. The 2, 3, 4, 5 and 6 nucleotide motifs were found for normal tissue ESTs whereas 5 nucleotide motifs were not found for tumoral tissue ESTs. ÖZKöpekler, insanlarla ortak bir çevreyi paylaşır ve belirli köpek ırklarının hastalıkları hakkında bilgi, insan kanser çalışmaları için bir model geliştirmede çok yararlıdır. EST'ler, bir organizmanın transkribe edilen genomunun bir parçasını temsil eder ve mikrosatellitleri tanımlamak için önemli bir kaynaktır. Tekrarlayan DNA dizilerini içeren Basit Dizi Tekrarları (SSR'ler) veya mikrosatellitler, bilinen en güçlü genetik belirteçler arasındadır. EST-SSR'lerin gelişimi, genomik çalışmalar için hızlı, verimli ve düşük maliyetli bir seçenek haline gelmiştir. Bu çalışmada, 2304 EST içeren Terrier köpeğin meme bezi dokusunun EST koleksiyonundan SSR'lerin belirlenmesi için; Web tabanlı sürümleri olan ve kolayca erişilebilen SSRIT ve IMEx yazılımları kullanılmıştır. SSRIT, 2 ila 10 baz uzunluğundaki motifleri bulur ve tekli nükleotid motiflerini ortadan kaldırarak minimum tekrar sayısını ayarlar. IMEx mükemmel ve kusurlu mikrosatellitleri ayrı ayrı bulur. Farklı uzunluklarda 1 ile 6 arasındaki motifleri bulabilir ve minimum tekrar sayısı ayarlanabilir. Ek olarak, istenen SSR bölgesi için uygun primer tasarlanabilir. Normal doku EST'leri için 2, 3, 4, 5 ve 6 nükleotidli motifler bulunurken, tümörlü doku EST'leri için 5 nükleotidli motif bulunamamıştır.

Introduction In the present study, RNA sequencing-mediated transcriptome analysis was performed in order to elucidate the molecular mechanisms of the immune response for different types of calorie restriction (CR) application using MMTV-TGF-α breast cancer mouse model. Methods Animals were applied to three different dietary regiments; ad libitum (AL), chronic calorie restriction (CCR) and intermittent calorie restriction (ICR). Using thymus tissues, 6091 differentially expressed genes (DEGs) were identified in three dietary groups. After clustering of total of 6091 DEGs using Gene Ontology (GO) categories, a total of 400 genes were identified to be involved in immune system process (GO:0002376) GO categories. KEGG pathway and gene co-expression network analysis of these immune-related DEGs were done using String database. The results were confirmed with measuring mRNA expression levels of four selected immune-related DEGs genes (Casp3, Thy1, IL-16 and CD4) using quantitative real-time PCR (qPCR). Results The expression levels of immune-related genes were different in three RNA-seq data. Conclusion The results provide useful information to investigate the immune-related transcriptional profiling in thymus tissue of breast cancer mouse model applied to two different types of CR and to identify the specific functional immune related genes in response to CR during cancer development.