We identify a total of 14,238 novel new transcribed regions corresponding to 12,597 new loci, as well as many novel transcript isoforms of previously annotated genes.
We have presented evidence that the pool size is dynamic with new transcribing minichromosomes entering the pool as a result of replication and old minichromosomes leaving the pool.
The identification of genes differentially expressed in Gu4 and Gu5 was performed combining two different statistical methods (see methods section) and using the gene annotations from the CGD, the new transcribed regions defined by previous studies [ 25- 27] and the new transcribed regions defined in this study (see above).
Because these transcripts have poor protein coding potential they likely represent new transcribed sequences derived from noncoding euchromatic regions or, alternatively, from regions of heterochromatin that are rich in complex satellite DNA repeats and other repetitive sequences (Akbari et al. 2013) (Table S8, Table S9, and Table S10).
Therefore, the TB repeats appear to be rearrangement elements within the genome that provide strong driving forces for the generation of new major transcribed CojaIIBs via duplications and/or transpositions.
We identified several new genes transcribed in response to nitrogen deprivation that have GO terms associated with regulation, including transcriptional regulators, two-component regulators, and kinases (Table 2 and additional file 1: Chromosome.xlsx).xlsx
The PIPSL gene (Akiva et al. 2006)—a new gene transcribed in the testis of humans and chimpanzees [ 202] provides an example of the kind of empirical evidence that would be relevant here.
Four other ESTs, two from mammary tumor (AW211687 and AW212179) and two from a forelimb of E13 embryo (CJ049248 and CR514396) were identified upstream of the 5' end of Pdcd2, suggesting there may be a new gene transcribed from the same promoter as Pdcd2, but in the opposite orientation.
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We conclude from these results that MCM, Cdc45, and PCNA maintenance on chromatin during S-phase is not dependent on the ability of CHO cells to continually transcribe new mRNA.
