Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins

Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a decrease in evolutionary rate implies constraint due to biological functionality. We found that our predicted coding fRNAs have a significant influence on evolutionary rates (especially at synonymous sites), independent of other functional measures. Thus, coding fRNA may play a role on sequence evolution. Given that coding regions of humans and flies contain many more predicted coding fRNAs than yeast, the impact of coding fRNAs on sequence evolution may be substantial in genomes of higher eukaryotes.     

Intercalary heterochromatin in polytene chromosomes of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Intercalary heterochromatin consists of extended chromosomal domains which are interspersed throughout the euchromatin and contain silent genetic material. These domains comprise either clusters of functionally unrelated genes or tandem gene duplications and possibly stretches of noncoding sequences. Strong repression of genetic activity means that intercalary heterochromatin displays properties that are normally attributable to classic pericentric heterochromatin: high compaction, late replication and underreplication in polytene chromosomes, and the presence of heterochromatin-specific proteins. Late replication and underreplication occurs when the suppressor of underreplication protein is present in intercalary heterochromatic regions. Intercalary heterochromatin underreplication in polytene chromosomes results in free double-stranded ends of DNA molecules; ligation of these free ends is the most likely mechanism for ectopic pairing between intercalary heterochromatic and pericentric heterochromatic regions. No support has been found for the view that the frequency of chromosome aberrations is elevated in intercalary heterochromatin.     

Role of paragenome in development

The concept of paragenome is proposed, which is considered as a transient array of short DNA molecules appearing on the chromosome surface during development for the control of genome. The paragenome consists of printomeres, chronomeres, and phylomeres. Chronomeres and printomeres are obligatory for cells of certain differentiation lineages, but the cells of different lineages differ in the sets of these organelles. Phylomeres are facultative, since they appear only when development is modified. The paragenome is a system governing the chromatin configuration and level of structural genes expression, ensuring the interpretation of positional information by the cells and their differentiation in regulatory morphogenesis, and controlling the development in time. Deciphering of the paragenome will allow realization in future of direct reprogramming of somatic cell nuclei without using stem cells and eggs.     

Role of paragenome in development

The concept of paragenome is proposed, which is considered as a transient array of short DNA molecules appearing on the chromosome surface during development for the control of genome. The paragenome consists of printomeres, chronomeres, and phylomeres. Chronomeres and printomeres are obligatory for cells of certain differentiation lineages, but the cells of different lineages differ in the sets of these organelles. Phylomeres are facultative, since they appear only when development is modified. The paragenome is a system governing the chromatin configuration and level of structural genes expression, ensuring the interpretation of positional information by the cells and their differentiation in regulatory morphogenesis, and controlling the development in time. Deciphering of the paragenome will allow realization in future of direct reprogramming of somatic cell nuclei without using stem cells and eggs.     

Cytogenetic and molecular aspects of position effect variegation in Drosophila melanogaster

A chromosomal region subjected to position effect variegation was analysed for possible DNA under-replication. DNA clones from the vicinity of the euheterochromatin junction and from a distance of hundreds of kilobase pairs were used as probes. Formation of compact blocks of chromatin is regarded as a characteristic feature of position effect variegation. It was shown that in T (1;2) dor ^var7 males undergoing position effect variegation clones representing the DNA nearest to the breakpoint in 2B7 hybridized normally in situ to the compact blocks, providing evidence against DNA underreplication. In females the same clones did not hybridize to the compact blocks. These variations in hybridization may be related to different degrees of compaction of chromosome regions in males and females. A correlation between the degree of underreplication and the level of cell polyteny was shown by Southern-blot hybridization of a DNA probe from the 2B region to DNA from an X/O strain carrying Dp (1;1)pn2b displaying position effect variegation and compaction in 94% of salivary gland cells. Almost complete underreplication of the DNA of this region was found in salivary gland cells (with a maximal degree of polyteny), intermediate underreplication was found in fat body cells (with an intermediate degree of polyteny), and replication was not disturbed in diploid cells of the larval cephalic complex.by W. Beermann     

A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication

Noncoding Y RNAs are required for the reconstitution of chromosomal DNA replication in late G1 phase template nuclei in a human cell-free system. Y RNA genes are present in all vertebrates and in some isolated nonvertebrates, but the conservation of Y RNA function and key determinants for its function are unknown. Here, we identify a determinant of Y RNA function in DNA replication, which is conserved throughout vertebrate evolution. Vertebrate Y RNAs are able to reconstitute chromosomal DNA replication in the human cell-free DNA replication system, but nonvertebrate Y RNAs are not. A conserved nucleotide sequence motif in the double-stranded stem of vertebrate Y RNAs correlates with Y RNA function. A functional screen of human Y1 RNA mutants identified this conserved motif as an essential determinant for reconstituting DNA replication in vitro. Double-stranded RNA oligonucleotides comprising this RNA motif are sufficient to reconstitute DNA replication, but corresponding DNA or random sequence RNA oligonucleotides are not. In intact cells, wild-type hY1 or the conserved RNA duplex can rescue an inhibition of DNA replication after RNA interference against hY3 RNA. Therefore, we have identified a new RNA motif that is conserved in vertebrate Y RNA evolution, and essential and sufficient for Y RNA function in human chromosomal DNA replication.     

A computational approach to identify genes for functional RNAs in genomic sequences

Currently there is no successful computational approach for identification of genes encoding novel functional RNAs (fRNAs) in genomic sequences. We have developed a machine learning approach using neural networks and support vector machines to extract common features among known RNAs for prediction of new RNA genes in the unannotated regions of prokaryotic and archaeal genomes. The Escherichia coli genome was used for development, but we have applied this method to several other bacterial and archaeal genomes. Networks based on nucleotide composition were 80–90% accurate in jackknife testing experiments for bacteria and 90–99% for hyperthermophilic archaea. We also achieved a significant improvement in accuracy by combining these predictions with those obtained using a second set of parameters consisting of known RNA sequence motifs and the calculated free energy of folding. Several known fRNAs not included in the training datasets were identified as well as several hundred predicted novel RNAs. These studies indicate that there are many unidentified RNAs in simple genomes that can be predicted computationally as a precursor to experimental study. Public access to our RNA gene predictions and an interface for user predictions is available via the web.     

Partial pneumonectomy of telomerase null mice carrying shortened telomeres initiates cell growth arrest resulting in a limited compensatory growth response

Telomerase mutations and significantly shortened chromosomal telomeres have recently been implicated in human lung pathologies. Natural telomere shortening is an inevitable consequence of aging, which is also a risk factor for development of lung disease. However, the impact of shortened telomeres and telomerase dysfunction on the ability of lung cells to respond to significant challenge is still largely unknown. We have previously shown that lungs of late generation, telomerase null B6.Cg-Terc(tm1Rdp) mice feature alveolar simplification and chronic stress signaling at baseline, a phenocopy of aged lung. To determine the role telomerase plays when the lung is challenged, B6.Cg-Terc(tm1Rdp) mice carrying shortened telomeres and wild-type controls were subjected to partial pneumonectomy. We found that telomerase activity was strongly induced in alveolar epithelial type 2 cells (AEC2) of the remaining lung immediately following surgery. Eighty-six percent of wild-type animals survived the procedure and exhibited a burst of early compensatory growth marked by upregulation of proliferation, stress response, and DNA repair pathways in AEC2. In B6.Cg-Terc(tm1Rdp) mice carrying shortened telomeres, response to pneumonectomy was characterized by decreased survival, diminished compensatory lung growth, attenuated distal lung progenitor cell response, persistent DNA damage, and cell growth arrest. Overall, survival correlated strongly with telomere length. We conclude that functional telomerase and properly maintained telomeres play key roles in both long-term survival and the early phase of compensatory lung growth following partial pneumonectomy.     

Cytophotometric studies on cells from the ovaries of otu mutants of Drosophila melanogaster

Amounts of chromosomal DNA were estimated for Feulgen-stained, ovarian cells from flies carrying certain mutant alleles of the otu (ovarian tumor) gene. Epithelial sheath cells and lumen cells were found to contain the diploid (2C) amount of DNA and therefore served as internal, cytophotometric standards. Mitotically active follicle cells over young tumors from homozygous otu1 females contained either the 2C or 4C amounts of DNA; whereas, the tumor cell population contained 2C, 4C and 8C nuclei and many intermediate values. Egg chambers also occur in homozygous otu7 females. Follicle cells above these oocytes undergo a maximum of four cycles of endomitotic DNA replication. The accompanying nurse cells (PNC) contain polytene chromosomes. These undergo a maximum of 12 endonuclear replication cycles. The PNCs show the expected levels of DNA for the first 6 cycles and the fraction failing to replicate during subsequent cycles may be as small as 10%. Lower than expected levels of DNA were detected in PNCs from an otu1/otu3 ovary, reflecting roughly 20% underreplication. The latter PNCs may have been interrupted before DNA synthesis was concluded. No simple model of genomic underreplication accounts for the several different patterns of DNA behavior observed for various otu mutants.     

Origins of G1 arrest in senescent human fibroblasts

Human diploid fibroblasts have a finite proliferative lifespan in culture, at the end of which they are ararrested with G₁ phase DNA contents. Upon serum stimulation, senescent cells are deficient in carrying out a subset of early signal transduction events such as activation of protein kinase C and induction of c-fos. Later in G₁, they uniformly fail to express late G₁ genes whose products are required for DNA synthesis, implying that they are unable to pass the R point. Failure to pass the R point may occur because senescent cells are unable to phosphorylate the retinoblastoma protein, owing to the accumulation of inactive complexes of cyclin E/Cdk2 and possibly cyclin D/Cdk4. Senescent cells contain high amounts of p21, a potent cyclin-dependent kinase inhibitor whose levels are also elevated in cells arrested in G₁ following DNA damage, suggesting that both arrests might share a common mechanism. Cell aging is accompanied by a progressive shortening of chromosomal telomeres, which could be perceived by the cells as a form of DNA damage that gives rise to the signals that inactivate the cell cycle machinery.     

Ribogenomics:the Science and Knowledge of RNA

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.     

Number of the repetitive euchromatic 5S RNA genes in polyploid tissues of Drosophila hydei

Repetitive genes localized within heterochromatin, such as the rDNA in Drosophila, replicate several steps less than the bulk DNA during polytenization. The 5S RNA genes of Drosophila hydei were chosen as a model system to inquire whether underreplication also occurs if the repetitive gene cluster is localized in the euchromatin. Filter saturation hybridization showed that there are 320 5S RNA gene copies in the haploid genome. Setting the diploid number at 100%, it was found that the DNA of polytene salivary glands reached only 79% of this value, and the DNA of polyploid ovarian tissue reached only 72% of this value. Although the latter two saturation values are less than the diploid standard, they are not as low as the 50% saturation value predicted for a one-step reduction. This may reflect a slower replication of these genes compared to the bulk DNA. These results imply that underreplication is not a general characteristic of repetitive genes but depends on their localization in the euchromatic or heterochromatic part of the genome.     

DNA underreplication in intercalary heterochromatin regions in polytene chromosomes of Drosophila melanogaster correlates with the formation of partial chromosomal aberrations and ectopic pairing

We studied the influence of the Suppressor of Underreplication (SuUR) gene expression on the intercalary heterochromatin (IH) regions of Drosophila melanogaster polytene chromosomes. We observed a strong positive correlation between increased SuUR expression, underreplication extent, amount of DNA truncation, and formation of ectopic contacts in IH regions. SuUR overexpression from heat shock-driven transgene results in the formation of partial chromosomal aberrations whose breakpoints map exclusively to the regions of intercalary and pericentric heterochromatin. It is important to note that all these effects are seen only if SuUR overexpression is induced during early stages of chromosome polytenization. Therefore, we developed the idea that ectopic pairing results from the joining of free DNA ends, which are formed as a consequence of underreplication.     

Cytophotometric studies on cells from the ovaries of otu mutants of Drosophila melanogaster

Summary Amounts of chromosomal DNA were estimated for Feulgen-stained, ovarian cells from flies carrying certain mutant alleles of the otu (ovarian tumor) gene. Epithelial sheath cells and lumen cells were found to contain the diploid (2C) amount of DNA and therefore served as internal, cytophotometric standards. Mitotically active follicle cells over young tumors-from homozygous otu ¹ females contained either the 2C or 4C amounts of DNA; whereas, the tumor cell population contained 2C, 4C and 8C nuclei and many intermediate values. Egg chambers also occur in homozygous otu ⁷ females. Follicle cells above these oocytes undergo a maximum of four cycles of endomitotic DNA replication. The accompanying nurse cells (PNC) contain polytene chromosomes. These undergo a maximum of 12 endonuclear replication cycles. The PNCs show the expected levels of DNA for the first 6 cycles and the fraction failing to replicate during subsequent cycles may be as small as 10%. Lower than expected levels of DNA were detected in PNCs from an otu ¹/otu ³ ovary, reflecting roughly 20% underreplication. The latter PNCs may have been interrupted before DNA synthesis was concluded. No simple model of genomic underreplication accounts for the several different patterns of DNA behavior observed for various otu mutants.     

cDNA genes formed after infection with retroviral vector particles lack the hallmarks of natural processed pseudogenes.

Retroviral proteins can encapsidate RNAs without retroviral cis-acting sequences. Such RNAs are reverse transcribed and inserted into the genomes of infected target cells to form cDNA genes. Previous investigations by Southern blot analysis of such cDNA genes suggested that they were truncated at the 3' and the 5' ends (R. Dornburg and H. M. Temin, Mol. Cell. Biol. 8:2328-2334, 1988). To analyze such cDNA genes further, we cloned three cDNA genes (derived from a hygromycin B phosphotransferase gene) in lambda vectors and analyzed them by DNA sequencing. We found that they did not correspond to the full-length mRNA: they were truncated at both the 3' and the 5' ends, did not contain a poly(A) tract, and were not flanked by direct repeats. The 3'-end junctions to chromosomal DNA of five more cDNA genes were amplified by polymerase chain reaction, cloned in pUC vectors, and sequenced. All of these cDNA genes had 3'-end truncations, and no poly(A) tracts were found. Further polymerase chain reaction experiments were performed to detect hygromycin B phosphotransferase cDNA genes with a poly(A) tract in DNA extracted from a pool of about 500 colonies of cells containing cDNA genes. No hygromycin B phosphotransferase cDNA gene with a poly(A) tract was found. Investigation of two preintegration sites by Southern analysis revealed that deletions were present in chromosomal DNA at the site of the integration of the cDNA genes. Naturally occurring processed pseudogenes correspond to the full-length mRNA, contain a poly(A) sequence, and are flanked by direct repeats. Our data indicate that cDNA genes formed by infection with retrovirus particles lack the hallmarks or natural processed pseudogenes. Thus, it appears that natural processed pseudogenes were not generated by retrovirus proteins.