Mammalian testis development is a complex and highly sophisticated process. To study the dynamic change of normal testis development at the transcriptional level, we investigated mouse testes at three postnatal ages: 6 days postnatal, 4 weeks old, and 10 weeks old, representing infant (PN1), juvenile (PN2), and adult (PN3) stages, respectively. Using ultra high-throughput RNA sequencing (RNA-seq) technology, we obtained 211 million reads with a length of 35 bp. We identified 18837 genes that were expressed in mouse testes, and found that genes expressed at the highest level were involved in spermatogenesis. The gene expression pattern in PN1 was distinct from that in PN2 and PN3, which indicates that spermatogenesis has commenced in PN2. We analyzed a large number of genes related to spermatogenesis and somatic development of the testis, which play important roles at different developmental stages. We also found that the MAPK, Hedgehog, and Wnt signaling pathways were significantly involved at different developmental stages. These findings further our understanding of the molecular mechanisms that regulate testis development. Our study also demonstrates significant advantages of RNA-seq technology for studying transcriptome during development.
GONG WeiPAN LinLinLIN QiangZHOU YuanYuanXIN ChengQiYU XiaoMinCUI PengHU SongNianYU Jun
An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancy-lactation-involution cycle （PL cycle） during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy （day 12 of pregnancy）, lactation （day 14 of lactation）, and involution （day 7 of involution）. The pregnancy-, lacta- tion- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs （ncRNAs）, respectively. Differentially expressed genes （DEGs） were defined in the three samples, which comprised 4843 DEGs （749 up-regulated and 4094 down-regulated） from pregnancy to lactation and 4926 DEGs （4706 up-regulated and 220 down-regulated） from lactation to involution. Besides the obvious and substantive up- and down-regulation of the DEGs, we observe that lysosomal enzymes were highly expressed and that their expression coin- cided with milk secretion. Further analysis of transcription factors such as Trpsl, Gtf2i, Tcf712, Nuprl, Vdr, Rbl, and Aebpl, and ncRNAs such as mir-125b, Let7, mir-146a, and mir-15 has enabled us to identify key regulators in mammary gland de- velopment and the PL cycle.
All eukaryotic genomes have genes with introns in variable sizes.As far as spliceosomal introns are concerned,there are at least three basic parameters to stratify introns across diverse eukaryotic taxa:size,number,and sequence context.The number parameter is highly variable in lower eukaryotes,especially among protozoan and fungal species,which ranges from less than4%to 78%of the genes.Over greater evolutionary time scales,the number parameter undoubtedly increases as observed in higher plants and higher vertebrates,reaching greater than 12.5 exons per gene in average among mammalian genomes.The size parameter is more complex,where multiple modes appear at work.Aside from intronless genes,there are three other types of intron-containing genes:half-sized,minimal,and size-expandable introns.The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes.Among the size-expandable introns,the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals,where the larger introns are filled with transposable elements and appear expansion-flexible,reaching several kilobasepairs(kbp)and even thousands of kbp in size.Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality.In particular,the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts.
WU JiaYanXIAO JingFaWANG LingPingZHONG JunYIN HongYanWU ShuangXiuZHANG ZhangYU Jun
Ribonucleic acid（RNA） deserves not only a dedicated field of biological research –– a discipline or branch of knowledge –– but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs（mRNAs） are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAembryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.
