Статті в журналах: "Cryptic elements"

1

Foster, E., J. Hattori, P. Zhang, H. Labbé, T. Martin-Heller, J. Li-Pook-Than, T. Ouellet, K. Malik, and B. Miki. "The new RENT family of repetitive elements in Nicotiana species harbors gene regulatory elements related to the tCUP cryptic promoter." Genome 46, no. 1 (February 1, 2003): 146–55. http://dx.doi.org/10.1139/g02-102.

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The tCUP cryptic constitutive promoter was discovered in the tobacco genome by T-DNA (transfer DNA) tagging with a promoterless GUSnos gene. Here, we show that the portion of the tCUP sequence containing a variety of cryptic gene regulatory elements is related to a new family of moderately repetitive sequences (102 copies), the RENT (repetitive element from Nicotiana tabacum) family. The RENT family is found only in certain Nicotiana species. Five RENT elements were cloned and sequenced. The RENT elements are a minimum of 5 kb in length and share 8090% sequence similarity throughout their length. The 5' termini are the same in the isolated RENT family members and are characterized by a conserved border sequence (TGTTGA(T or C)ACCCAATTTT(T or C)). The 3' ends of RENT sequence similarity vary in location and sequence. The tCUP cryptic promoter originated from a unique truncated RENT element that interrupts a phytochelatin synthase-like gene that may have undergone rearrangements prior to or resulting from T-DNA insertion. No evidence was found for expressed coding regions within the RENT elements; however, like the cryptic gene regulatory elements within the tCUP sequence, the isolated RENT elements possess promoter activity and translational enhancer activity.Key words: cryptic promoter, Nicotiana, T-DNA, translational enhancer, repetitive element.

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2

Fedoroff, N. "The heritable activation of cryptic Suppressor-mutator elements by an active element." Genetics 121, no. 3 (March 1, 1989): 591–608. http://dx.doi.org/10.1093/genetics/121.3.591.

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Abstract A weakly active maize Suppressor-mutator (Spm-omega) element is able to heritably activate cryptic Spm elements in the maize genome. The spontaneous activation frequency, which is 1-5 x 10(-5) in the present genetic background, increases by about 100-fold in the presence of an Spm-omega and remains an order of magnitude above the background level a generation after removal of the activating Spm-omega. Sectorial somatic reactivation of cryptic elements can be detected phenotypically in kernels. Selection of such kernels constitutes an efficient selection for plants with reactivated Spm elements. Analysis of the reactivation process reveals that it is gradual and proceeds through genetically metastable intermediates that exhibit different patterns of element expression during plant development. Newly reactivated elements tend to return to an inactive form. However, the probability that an element will remain in a heritably active state increases when the element is maintained in the presence of an active Spm element for several generations.

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3

Moorefield, Beth. "Cryptic elements of the heat-shock response." Nature Structural & Molecular Biology 29, no. 3 (March 2022): 189. http://dx.doi.org/10.1038/s41594-022-00752-4.

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4

Vorechovsky, Igor. "Transposable elements in disease-associated cryptic exons." Human Genetics 127, no. 2 (October 10, 2009): 135–54. http://dx.doi.org/10.1007/s00439-009-0752-4.

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5

Prieur, D., G. Erauso, C. Geslin, S. Lucas, M. Gaillard, A. Bidault, A. C. Mattenet, et al. "Genetic elements of Thermococcales." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 184–87. http://dx.doi.org/10.1042/bst0320184.

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This minireview summarizes our current knowledge about archaeal genetic elements in the hyperthermophilic order Thermococcales in the phylum Euryarchaeota. This includes recent work on the first virus of Pyrococcus, PAV1, the discovery of novel unique virus morphotypes in hot deep-sea environments, and preliminary observations on novel cryptic plasmids. We also review the work accomplished over the last 5 years in the development of genetic tools for members of the Pyrococcus and Thermococcus genera, mainly in our laboratories.

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6

Hecht, Katrin, James E. Bailey, and Wolfgang Minas. "Polycistronic gene expression in yeast versus cryptic promoter elements." FEMS Yeast Research 2, no. 2 (May 2002): 215–24. http://dx.doi.org/10.1111/j.1567-1364.2002.tb00086.x.

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7

HECHT, K., J. BAILEY, and W. MINAS. "Polycistronic gene expression in yeast versus cryptic promoter elements." FEMS Yeast Research 2, no. 2 (May 2002): 215–24. http://dx.doi.org/10.1016/s1567-1356(02)00085-5.

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8

Fedoroff, Nina, Jo Ann Banks, and Patrick Masson. "Molecular genetic analysis of the maize Suppressor-mutator element's epigenetic developmental regulatory mechanism." Genome 31, no. 2 (January 15, 1989): 973–79. http://dx.doi.org/10.1139/g89-170.

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The genetic mechanism underlying the developmental regulation of the maize Suppressor-mutator element has been analyzed by molecular and genetic techniques. The element is subject to inactivation by a negative, epigenetic mechanism that results in the methylation of C residues in the vicinity of the element's transcription start site. Fully methylated elements are genetically and transcriptionally silent (cryptic), while hypomethylated elements are active. Partially methylated elements, designated programable, exhibit a variety of developmental expression programs. The element encodes a positive regulatory gene product which activates element expression and promotes reprograming of the element by interfering with methylation of the element's 5′ end.Key words: maize transposable element, Suppressor-mutator element, developmental regulation.

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9

Li, Liqiang, Jianning Liu, Qiong Zhang, Runying Fu, Xiwu Zhu, Chao Li, and Jishuang Chen. "Seed-borne viral dsRNA elements in three cultivatedRaphanusandBrassicaplants suggest three cryptoviruses." Canadian Journal of Microbiology 62, no. 4 (April 2016): 287–95. http://dx.doi.org/10.1139/cjm-2015-0788.

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Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these cryptoviruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed.

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10

Domenjoud, L., H. Gallinaro, L. Kister, S. Meyer, and M. Jacob. "Identification of a specific exon sequence that is a major determinant in the selection between a natural and a cryptic 5' splice site." Molecular and Cellular Biology 11, no. 9 (September 1991): 4581–90. http://dx.doi.org/10.1128/mcb.11.9.4581-4590.1991.

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The first intron of the early region 3 from adenovirus type 2 contains a cryptic 5' splice site, Dcr1, 74 nucleotides downstream from the natural site D1. The cryptic site can be activated when the natural site is inactivated by mutagenesis. To investigate the basis for selection between a natural and a cryptic 5' splice site, we searched for cis-acting elements responsible for the exclusive selection of the natural site. We show that both the relative intrinsic strength of the sites and the sequence context affect the selection. A 120-nucleotide segment located at the 3' end of exon 1 enhances splicing at the proximal site D1; in its absence the two sites are used according to their strength. Thus, three cis-acting elements are involved in the silencing of the cryptic site: the sequence of D1, the sequence of Dcr1, and an upstream exonic sequence. We show that the exonic element folds, in solution, into a 113-nucleotide-long stem-loop structure. We propose that this potential stem-loop structure which is located 6 nucleotides upstream of the exon 1-intron junction is responsible for the preferential use of the natural 5' splice site.

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11

Domenjoud, L., H. Gallinaro, L. Kister, S. Meyer, and M. Jacob. "Identification of a specific exon sequence that is a major determinant in the selection between a natural and a cryptic 5' splice site." Molecular and Cellular Biology 11, no. 9 (September 1991): 4581–90. http://dx.doi.org/10.1128/mcb.11.9.4581.

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The first intron of the early region 3 from adenovirus type 2 contains a cryptic 5' splice site, Dcr1, 74 nucleotides downstream from the natural site D1. The cryptic site can be activated when the natural site is inactivated by mutagenesis. To investigate the basis for selection between a natural and a cryptic 5' splice site, we searched for cis-acting elements responsible for the exclusive selection of the natural site. We show that both the relative intrinsic strength of the sites and the sequence context affect the selection. A 120-nucleotide segment located at the 3' end of exon 1 enhances splicing at the proximal site D1; in its absence the two sites are used according to their strength. Thus, three cis-acting elements are involved in the silencing of the cryptic site: the sequence of D1, the sequence of Dcr1, and an upstream exonic sequence. We show that the exonic element folds, in solution, into a 113-nucleotide-long stem-loop structure. We propose that this potential stem-loop structure which is located 6 nucleotides upstream of the exon 1-intron junction is responsible for the preferential use of the natural 5' splice site.

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12

Breton, Marc, Florence Tardy, Emilie Dordet-Frisoni, Eveline Sagne, Virginie Mick, Joël Renaudin, Pascal Sirand-Pugnet, Christine Citti, and Alain Blanchard. "Distribution and diversity of mycoplasma plasmids: lessons from cryptic genetic elements." BMC Microbiology 12, no. 1 (2012): 257. http://dx.doi.org/10.1186/1471-2180-12-257.

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13

Lei, Haixin, and Igor Vořechovský. "Identification of Splicing Silencers and Enhancers in Sense Alus: a Role for Pseudoacceptors in Splice Site Repression." Molecular and Cellular Biology 25, no. 16 (August 15, 2005): 6912–20. http://dx.doi.org/10.1128/mcb.25.16.6912-6920.2005.

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ABSTRACT Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3′ splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.

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14

Verma, Bhupendra, Anand Ponnuswamy, Sivakumar Vadivel Gnanasundram, and Saumitra Das. "Cryptic AUG is important for 48S ribosomal assembly during internal initiation of translation of coxsackievirus B3 RNA." Journal of General Virology 92, no. 10 (October 1, 2011): 2310–19. http://dx.doi.org/10.1099/vir.0.032151-0.

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We have investigated the possible role of a conserved cis-acting element, the cryptic AUG, present in the 5′ UTR of coxsackievirus B3 (CVB3 ) RNA. CVB3 5′ UTR contains multiple AUG codons upstream of the initiator AUG, which are not used for the initiation of translation. The 48S ribosomal assembly takes place upstream of the cryptic AUG. We show here that mutation in the cryptic AUG results in reduced efficiency of translation mediated by the CVB3 IRES; mutation also reduces the interaction of mutant IRES with a well characterized IRES trans-acting factor, the human La protein. Furthermore, partial silencing of the La gene showed a decrease in IRES activity in the case of both the wild-type and mutant. We have demonstrated here that the interaction of the 48S ribosomal complex with mutant RNA was weaker compared with wild-type RNA by ribosome assembly analysis. We have also investigated by chemical and enzymic modifications the possible alteration in secondary structure in the mutant RNA. Results suggest that the secondary structure of mutant RNA was only marginally altered. Additionally, we have demonstrated by generating compensatory and non-specific mutations the specific function of the cryptic AUG in internal initiation. Results suggest that the effect of the cryptic AUG is specific and translation could not be rescued. However, a possibility of tertiary interaction of the cryptic AUG with other cis-acting elements cannot be ruled out. Taken together, it appears that the integrity of the cryptic AUG is important for efficient translation initiation by the CVB3 IRES RNA.

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15

Bowden, Steven D., та George P. C. Salmond. "Exploitation of a β-lactamase reporter gene fusion in the carbapenem antibiotic production operon to study adaptive evolution in Erwinia carotovora". Microbiology 152, № 4 (1 квітня 2006): 1089–97. http://dx.doi.org/10.1099/mic.0.28575-0.

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Erwinia carotovora subsp. carotovora strain ATTn10 produces the β-lactam antibiotic 1-carbapen-2-em-3-carboxylic acid (carbapenem) by expressing the carABCDEFGH operon. Mutants exhibiting increased carbapenem gene transcription were positively selected using an engineered strain with a functional β-lactamase translational fusion in carH, the last gene of the operon. However, spontaneous ampicillin-resistant mutants were isolated even when transcription of carH : : blaM was blocked by a strongly polar mutation in carE. The mechanism of resistance was shown to be due to cryptic IS10 elements transposing upstream of carH : : blaM, thereby providing new promoters enabling carH : : blaM transcription. Southern blots showed that IS10 was present in multicopy in ATTn10. In addition, a Tn10 genetic remnant was discovered. The results offer insights into the genetic archaeology of strain ATTn10 and highlight the powerful impacts of cryptic IS elements in bacterial adaptive evolution.

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16

Tian, Lining, Keqiang Wu, Caroline Levasseur, Thérèse Ouellet, Elizabeth Foster, Marysia Latoszek-Green, Susan Sibbald, Brian Miki, Armand Seguin, and Daniel C. W. Brown. "Activity of elements from the tobacco cryptic promoter, tCUP, in conifer tissues." In Vitro Cellular & Developmental Biology - Plant 39, no. 2 (March 2003): 193–202. http://dx.doi.org/10.1079/ivp2002365.

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17

Adeel, Muhammad, Jie Yinn Lee, Muhammad Zain, Muhammad Rizwan, Aamir Nawab, M. A. Ahmad, Muhammad Shafiq, et al. "Cryptic footprints of rare earth elements on natural resources and living organisms." Environment International 127 (June 2019): 785–800. http://dx.doi.org/10.1016/j.envint.2019.03.022.

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18

Malik, K., K. Wu, X. Q. Li, T. Martin-Heller, M. Hu, E. Foster, L. Tian, et al. "A constitutive gene expression system derived from the tCUP cryptic promoter elements." Theoretical and Applied Genetics 105, no. 4 (September 2002): 505–14. http://dx.doi.org/10.1007/s00122-002-0926-0.

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19

Murakami, Nobuya, Ai Kurogi, Satoshi O. Suzuki, Takafumi Shimogawa, Nobutaka Mukae, Koji Yoshimoto, and Takato Morioka. "Histopathological presence of dermal elements in resected margins of neural structures obtained from initial repair surgery for myelomeningocele." Surgical Neurology International 14 (January 6, 2023): 7. http://dx.doi.org/10.25259/sni_989_2022.

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Background: Development of dermoid or epidermoid cysts in myelomeningocele (MMC) sites is generally thought to occur in a delayed fashion due to implantation of dermal elements during initial repair surgery. Another theory is that dermal and dermoid elements may already be present within dysplastic neural structures at birth. Methods: We experienced histopathological presence of dermal elements in resected tissues at initial repair surgery in four out of 18 cases with MMC who required resection of parts or margins of the neural structures to perform cord untethering. Since one of these cases has already been reported, we describe the clinicopathological findings for the remaining three cases. Results: In Case1, cryptic dermoid elements were discovered in the terminal filum-like structure (FT-LS) caudal to the open neural placode (NP). The FT-LS had histopathological characteristics similar to the retained medullary cord. In Case 2, dermoid elements were discovered in the caudal margin of the dysplastic conus medullaris. In Case 3, a thin squamous epithelial layer overlapped the rostral margin of the NP where the NP was located near the skin. Case 1 developed an epidermoid cyst at 1 year and 2 months of age, which was totally resected. Conclusion: Prenatally existing cryptic dermoid elements in the caudal portion of neural structures and remnants of dermal elements overlapping the rostral margin of the NP are associated with delayed occurrence of dermoid/ epidermoid cysts. Postoperative histopathological investigation of the resected specimens is recommended. Once dermal elements are revealed, repeated imaging examination and additional surgery should be considered.

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20

Joseph, Brian, and Eric C. Lai. "The Exon Junction Complex and intron removal prevent re-splicing of mRNA." PLOS Genetics 17, no. 5 (May 25, 2021): e1009563. http://dx.doi.org/10.1371/journal.pgen.1009563.

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Accurate splice site selection is critical for fruitful gene expression. Recently, the mammalian EJC was shown to repress competing, cryptic, splice sites (SS). However, the evolutionary generality of this remains unclear. Here, we demonstrate the Drosophila EJC suppresses hundreds of functional cryptic SS, even though most bear weak splicing motifs and are seemingly incompetent. Mechanistically, the EJC directly conceals cryptic splicing elements by virtue of its position-specific recruitment, preventing aberrant SS definition. Unexpectedly, we discover the EJC inhibits scores of regenerated 5’ and 3’ recursive SS on segments that have already undergone splicing, and that loss of EJC regulation triggers faulty resplicing of mRNA. An important corollary is that certain intronless cDNA constructs yield unanticipated, truncated transcripts generated by resplicing. We conclude the EJC has conserved roles to defend transcriptome fidelity by (1) repressing illegitimate splice sites on pre-mRNAs, and (2) preventing inadvertent activation of such sites on spliced segments.

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21

Kupriyanova, L. A., and L. D. Safronova. "Results and perspectives of cyto- and genetic studying of “cryptic” group of the Lacertidae." Proceedings of the Zoological Institute RAS 324, no. 1 (March 24, 2020): 100–107. http://dx.doi.org/10.31610/trudyzin/2020.324.1.100.

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Results of chromosomal and molecular studies of the lizard Zootoca vivipara (Lichtenstein, 1823) (Lacertidae) from many geographically separate populations of Europe and Asia have been generalized. The questions of karyotype differences within the species, of diversity of its Zw and multiple Z1Z2W sex chromosome, their reorganizations and evolutionary consequences have been briefly considered. Stability of forming karyotypes is as an integrating factor which allow to identify the specimens and unite them into the groups possessing the distinct distribution areas. There are a correlation between chromosomal, mt DNA and nuclear DNA data. Finally all data obtained allow to draw a conclusion that Z. vivipara represents a cryptic group of cryptic taxa. Besides new data about the behavior of multiple sex chromosomes (SC, synaptonemal complexes) in early meiosis and molecular-cytogenetic data on transposable elements (TE) in the genome of Z. vivipara, their localization in the definite regions of chromosomes may suggest that they play a role in active speciation process by formation of cryptic taxa.

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22

Xu, Jingsong, Dorothy Rodriguez, Eric Petitclerc, Jenny J. Kim, Masanori Hangai, S. Moon Yuen, George E. Davis, and Peter C. Brooks. "Proteolytic exposure of a cryptic site within collagen type IV is required for angiogenesis and tumor growth in vivo." Journal of Cell Biology 154, no. 5 (September 3, 2001): 1069–80. http://dx.doi.org/10.1083/jcb.200103111.

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Evidence is provided that proteolytic cleavage of collagen type IV results in the exposure of a functionally important cryptic site hidden within its triple helical structure. Exposure of this cryptic site was associated with angiogenic, but not quiescent, blood vessels and was required for angiogenesis in vivo. Exposure of the HUIV26 epitope was associated with a loss of α1β1 integrin binding and the gain of αvβ3 binding. A monoclonal antibody (HUIV26) directed to this site disrupts integrin-dependent endothelial cell interactions and potently inhibits angiogenesis and tumor growth. Together, these studies suggest a novel mechanism by which proteolysis contributes to angiogenesis by exposing hidden regulatory elements within matrix-immobilized collagen type IV.

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23

Rebelo, Adriana P., Alexander J. Abrams, Ellen Cottenie, Alejandro Horga, Michael Gonzalez, Dana M. Bis, Avencia Sanchez-Mejias, et al. "Cryptic Amyloidogenic Elements in the 3′ UTRs of Neurofilament Genes Trigger Axonal Neuropathy." American Journal of Human Genetics 98, no. 4 (April 2016): 597–614. http://dx.doi.org/10.1016/j.ajhg.2016.02.022.

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24

Tanoeiro, Luís, Mónica Oleastro, Alexandra Nunes, Andreia T. Marques, Sílvia Vaz Duarte, João Paulo Gomes, António Pedro Alves Matos, Jorge M. B. Vítor, and Filipa F. Vale. "Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression." Microorganisms 10, no. 3 (February 26, 2022): 516. http://dx.doi.org/10.3390/microorganisms10030516.

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Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression events and consequent impact on host ecology and evolution remain elusive. Three distinct prophages, named C. jejuni integrated elements 1, 2, and 4 (CJIE1, CJIE2, and CJIE4), are described in C. jejuni. Here, we identified two unreported prophages, Campylobacter coli integrated elements 1 and 2 (CCIE1 and CCIE2 prophages), which are C. coli homologues of CJIE1 and CJIE2, respectively. No induction was achieved for both prophages. Conversely, induction assays on CJIE1 and CJIE2 point towards the inducibility of these prophages. CCIE2-, CJIE1-, and CJIE4-like prophages were identified in a Campylobacter spp. population of 840 genomes, and phylogenetic analysis revealed clustering in three major groups: CJIE1-CCIE1, CJIE2-CCIE2, and CJIE4, clearly segregating prophages from C. jejuni and C. coli, but not from human- and nonhuman-derived isolates, corroborating the flowing between animals and humans in the agricultural context. Punctual bacteriophage host-jumps were observed in the context of C. jejuni and C. coli, and although random chance cannot be fully discarded, these observations seem to implicate prophages in evolutionary introgression events that are modulating the hybridization of C. jejuni and C. coli species.

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25

Shoemaker, N. B., and A. A. Salyers. "A cryptic 65-kilobase-pair transposonlike element isolated from Bacteroides uniformis has homology with Bacteroides conjugal tetracycline resistance elements." Journal of Bacteriology 172, no. 4 (1990): 1694–702. http://dx.doi.org/10.1128/jb.172.4.1694-1702.1990.

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26

Kobluk, David R., and Mary A. Lysenko. "Impact of two sequential Pacific hurricanes on sub-rubble cryptic corals: the possible role of cryptic organisms in maintenance of coral reef communities." Journal of Paleontology 61, no. 4 (July 1987): 663–75. http://dx.doi.org/10.1017/s0022336000029024.

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The hermatypic scleractinian cryptic coral biota living under mobile rubble in the reef flat and back reef zones of a Fijian fringing reef was surveyed in detail in August of 1984; only 138 days later the reef was struck by the first of two sequential hurricanes (57 days apart). The same sample areas were re-studied in August 1985, thereby providing the first detailed census of pre- and post-hurricane cryptic reef coral populations, and allowing an assessment of hurricane impact on these populations.The 61 cryptic species (60 corals and Millepora) show 88 percent commonality with the intertidal and shallow subtidal reef surface coral population (68 species), and therefore are a good representation of the surface biota.A major effect of the hurricanes was a reduction of almost 50 percent in the number of boulders sheltering cryptic coral. However, among boulders that retained coral through the storms, there was only a 5 percent reduction in the mean number of corals per boulder, signifying that damage to the surviving population was minor. The composition of the surviving cryptic coral population is essentially unchanged from its pre-hurricane state (there are differences in absolute abundances), and the relative importance of the species does not show marked change in most cases. Coral morphologies show little change in their absolute and relative percent abundances after the hurricanes. In contrast to what is normally seen in reef surface habitats, therefore, coral colony form did not appear to be an important determinant in survivability for those living under boulders; primary selection by the storms seems to have been on boulder form rather than cryptic coral form.Cryptic sub-rubble coral populations may function as a preserve for elements of the pre-hurricane reef surface community. For example, delicately-branching forms that are commonly devastated in reef surface habitats during hurricanes may, in some cases, be preserved in great numbers under boulders or in other cryptic habitats. This provides a “recruitment pool” that can greatly accelerate their recovery and re-establishment on the post-hurricane reef surface, and dampen the potentially severe community dislocations arising from intense competition for space in “instantaneous” new reef substrate.

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27

Hicks, Martin, Ryan Fink, and Flobater Gawargi. "EXTH-26. SECONDARY STRUCTURE ANALYSIS OF THE EGFR PRE-mRNA TRANSCRIPT TO IDENTIFY TARGETABLE REGIONS AND OPTIMIZE RNA THERAPY." Neuro-Oncology 22, Supplement_2 (November 2020): ii92. http://dx.doi.org/10.1093/neuonc/noaa215.380.

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Abstract Individuals diagnosed with glioblastoma multiforme (GBM) have a short life expectancy of 12–15 months. Current strategies are often limited by the blood-brain barrier. This project is to develop therapies to bypass challenges to effective and continuous drug delivery to the brain, targeting cancer-driving genes. Epidermal growth factor receptor (EGFR) is dysregulated in 57% of all GBM. Our approach uses an adeno-associated virus gene transfer vector encoding RNA therapeutics targeting critical elements of the EGFR pre-mRNA transcript. The ‘pre-mRNA structurome’ can be used to uncover and determine the accessibility of targetable regions. Our approach has the potential to deliver one single dose of gene therapy directly to the GBM tumor environment and block the production of EGFR and activate the expression of a stable therapeutic isoform of EGFR. To advance our therapeutic strategy, we have analyzed the EGFR secondary structure using selective 2’ hydroxyl acylation and primer extension followed by mutational profiling (SHAPE-MaP). SHAPE-MaP reactivity profiles were generated revealing the structure of splicing and cryptic polyadenylation signal (PAS) elements within the targeted region. We identified enhancer binding motifs surrounding the 5’ splice site and hidden elements of the cryptic PAS. Based on these structural profiles, we generated RNA therapies to unravel the hidden PAS to activate expression of the short therapeutic isoform.

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28

Lipps, G. "The replication protein of the Sulfolobus islandicus plasmid pRN1." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 240–44. http://dx.doi.org/10.1042/bst0320240.

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The thermoacidophile crenarchaeote Sulfolobus ssp. is one of the best-studied Archaea. Cryptic and conjugative plasmids as well as viruses have been described for this genus. For the majority of the genetic elements only the genome sequence and the basic characteristics were determined. In contrast the fusellovirus SSV1 and the cryptic plasmid pRN1, which is the smallest known genetic element of the crenarchaeota, have been studied in more detail. The three gene products of the plasmid pRN1 have been characterized biochemically. The replication protein of the plasmid, a multifunctional enzyme, has a novel domain, termed prim/pol domain. This domain constitutes the first member of the DNA polymerase family E. Based on the biochemical characterization of the gene products a model of how pRN1 is replicated in vivo is proposed.

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29

Ortiz-Severín, Javiera, Dante Travisany, Alejandro Maass, Francisco P. Chávez, and Verónica Cambiazo. "Piscirickettsia salmonis Cryptic Plasmids: Source of Mobile DNA and Virulence Factors." Pathogens 8, no. 4 (November 28, 2019): 269. http://dx.doi.org/10.3390/pathogens8040269.

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Four large cryptic plasmids were identified in the salmon pathogen Piscirickettsia salmonis reference strain LF-89. These plasmids appeared highly novel, with less than 7% nucleotidic identity to the nr plasmid database. Plasmid copy number analysis revealed that they are harbored in chromosome equivalent ratios. In addition to plasmid-related genes (plasmidial autonomous replication, partitioning, maintenance, and mobilization genes), mobile genetic elements such as transposases, integrases, and prophage sequences were also identified in P. salmonis plasmids. However, bacterial lysis was not observed upon the induction of prophages. A total of twelve putative virulence factors (VFs) were identified, in addition to two global transcriptional regulators, the widely conserved CsrA protein and the regulator Crp/Fnr. Eleven of the putative VFs were overexpressed during infection in two salmon-derived cellular infection models, supporting their role as VFs. The ubiquity of these plasmids was also confirmed by sequence similarity in the genomes of other P. salmonis strains. The ontology of P. salmonis plasmids suggests a role in bacterial fitness and adaptation to the environment as they encode proteins related to mobilization, nutrient transport and utilization, and bacterial virulence. Further functional characterization of P. salmonis plasmids may improve our knowledge regarding virulence and mobile elements in this intracellular pathogen.

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30

McCullough, A. J., H. Lou, and M. A. Schuler. "Factors affecting authentic 5' splice site selection in plant nuclei." Molecular and Cellular Biology 13, no. 3 (March 1993): 1323–31. http://dx.doi.org/10.1128/mcb.13.3.1323-1331.1993.

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To define elements critical for 5' splice selection in dicot plant nuclei, wild-type and mutant transcripts containing the first intron of the pea rbcS3A gene were expressed in vivo by using an autonomously replicating plant expression vector. Mutations within the normal 5' splice site (+1) of this intron demonstrate that 5' splice sites at the normal exon-intron boundary having only limited agreement with a 5' splice site consensus sequence can be spliced quite effectively in dicot nuclei. Inactivation of the normal 5' splice site occurs only by point mutations of the G at position +1 of the intron (+1G) or +2U or by multiple mutations at other positions and results in the activation of three cryptic 5' splice sites in the adjacent exon and intron. cis competition of cryptic sites having consensus 5' splice site sequences with the normal 5' splice site demonstrates that cryptic splice sites in the exon, but not the intron, can compete to some extent with the normal site. Replacement of the sequences between the cryptic and normal 5' splice sites with heterologous exon or intron sequences demonstrates that the 5' boundary of this plant intron is defined by its position relative to the AU transition point between exon and intron. These results suggest that potential 5' splice sites upstream of the AU transition point are accessible for recognition by the plant pre-mRNA splicing machinery and that those downstream in the AU-rich intron are masked from recognition.

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31

McCullough, A. J., H. Lou, and M. A. Schuler. "Factors affecting authentic 5' splice site selection in plant nuclei." Molecular and Cellular Biology 13, no. 3 (March 1993): 1323–31. http://dx.doi.org/10.1128/mcb.13.3.1323.

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Анотація:

To define elements critical for 5' splice selection in dicot plant nuclei, wild-type and mutant transcripts containing the first intron of the pea rbcS3A gene were expressed in vivo by using an autonomously replicating plant expression vector. Mutations within the normal 5' splice site (+1) of this intron demonstrate that 5' splice sites at the normal exon-intron boundary having only limited agreement with a 5' splice site consensus sequence can be spliced quite effectively in dicot nuclei. Inactivation of the normal 5' splice site occurs only by point mutations of the G at position +1 of the intron (+1G) or +2U or by multiple mutations at other positions and results in the activation of three cryptic 5' splice sites in the adjacent exon and intron. cis competition of cryptic sites having consensus 5' splice site sequences with the normal 5' splice site demonstrates that cryptic splice sites in the exon, but not the intron, can compete to some extent with the normal site. Replacement of the sequences between the cryptic and normal 5' splice sites with heterologous exon or intron sequences demonstrates that the 5' boundary of this plant intron is defined by its position relative to the AU transition point between exon and intron. These results suggest that potential 5' splice sites upstream of the AU transition point are accessible for recognition by the plant pre-mRNA splicing machinery and that those downstream in the AU-rich intron are masked from recognition.

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32

Han, XiangHua, Jennifer M. Caron, and Peter C. Brooks. "Cryptic collagen elements as signaling hubs in the regulation of tumor growth and metastasis." Journal of Cellular Physiology 235, no. 12 (May 12, 2020): 9005–20. http://dx.doi.org/10.1002/jcp.29752.

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33

Futcher, B., E. Reid, and D. A. Hickey. "Maintenance of the 2 micron circle plasmid of Saccharomyces cerevisiae by sexual transmission: an example of a selfish DNA." Genetics 118, no. 3 (March 1, 1988): 411–15. http://dx.doi.org/10.1093/genetics/118.3.411.

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Abstract Many eukaryotic mobile elements have been identified, but few have any obvious function. This has led to the proposal that many such elements may be parasitic DNA. We have used the 2 micron circle plasmid of Saccharomyces cerevisiae as a model system to investigate the maintenance of a cryptic genetic element. We find that under certain conditions this plasmid can spread through experimental populations despite demonstrable selection against it. This spread is dependent upon outbreeding, suggesting that cell to cell transmission of the plasmid during the yeast sexual cycle can counterbalance selection, and maintain the plasmid in populations. This result provides experimental support for the idea that some mobile elements may be parasitic DNA.

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34

Ram, Oren, Schraga Schwartz, and Gil Ast. "Multifactorial Interplay Controls the Splicing Profile of Alu-Derived Exons." Molecular and Cellular Biology 28, no. 10 (March 10, 2008): 3513–25. http://dx.doi.org/10.1128/mcb.02279-07.

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ABSTRACT Exonization of Alu elements creates primate-specific genomic diversity. Here we combine bioinformatic and experimental methodologies to reconstruct the molecular changes leading to exon selection. Our analyses revealed an intricate network involved in Alu exonization. A typical Alu element contains multiple sites with the potential to serve as 5′ splice sites (5′ss). First, we demonstrated the role of 5′ss strength in controlling exonization events. Second, we found that a cryptic 5′ss enhances the selection of a more upstream site and demonstrate that this is mediated by binding of U1 snRNA to the cryptic splice site, challenging the traditional role attributed to U1 snRNA of binding the 5′ss only. Third, we used a simple algorithm to identify specific sequences that determine splice site selection within specific Alu exons. Finally, by inserting identical exons within different sequences, we demonstrated the importance of flanking genomic sequences in determining whether an Alu exon will undergo exonization. Overall, our results demonstrate the complex interplay between at least four interacting layers that affect Alu exonization. These results shed light on the mechanism through which Alu elements enrich the primate transcriptome and allow a better understanding of the exonization process in general.

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35

Brown, D. C. W., L. Tian, S. Sibbald, M. Latoszek-Green, B. L. Miki, T. Ouellet, K. Wu, et al. "CRYPTIC GENETIC ELEMENTS FOR REGULATION OF GENE EXPRESSION IN PLANTS: THE tCUP GENE EXPRESSION SYSTEM." Acta Horticulturae, no. 560 (October 2001): 51–54. http://dx.doi.org/10.17660/actahortic.2001.560.4.

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36

Hanawa, Hideki, Derek A. Persons, and Arthur W. Nienhuis. "Mobilization and Mechanism of Transcription of Integrated Self-Inactivating Lentiviral Vectors." Journal of Virology 79, no. 13 (July 1, 2005): 8410–21. http://dx.doi.org/10.1128/jvi.79.13.8410-8421.2005.

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ABSTRACT Permanent genetic modification of replicating primitive hematopoietic cells by an integrated vector has many potential therapeutic applications. Both oncoretroviral and lentiviral vectors have a predilection for integration into transcriptionally active genes, creating the potential for promoter activation or gene disruption. The use of self-inactivating (SIN) vectors in which a deletion of the enhancer and promoter sequences from the 3′ long terminal repeat (LTR) is copied over into the 5′ LTR during vector integration is designed to improve safety by reducing the risk of mobilization of the vector genome and the influence of the LTR on nearby cellular promoters. Our results indicate that SIN vectors are mobilized in cells expressing lentiviral proteins, with the frequency of mobilization influenced by features of the vector design. The mechanism of transcription of integrated vector genomes was evaluated using a promoter trap design with a vector encoding tat but lacking an upstream promoter in a cell line in which drug resistance depended on tat expression. In six clones studied, all transcripts originated from cryptic promoters either upstream or within the vector genome. We estimate that approximately 1 in 3,000 integrated vector genomes is transcribed, leading to the inference that activation of cryptic promoters must depend on local features of chromatin structure and the constellation of nearby regulatory elements as well as the nature of the regulatory elements within the vector.

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37

Joyce, Nicholas, Daniel Layton-Matthews, Kurt Kyser, Matthew Leybourne, Kevin Ansdell, Tom Kotzer, David Quirt, and Gerard Zaluski. "Alteration mineralogy and pathfinder element inventory in the footprint of the McArthur River unconformity-related uranium deposit, Canada." Canadian Mineralogist 59, no. 5 (September 1, 2021): 985–1019. http://dx.doi.org/10.3749/canmin.2000067.

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ABSTRACT Pathfinder elements associated with the exploration footprint of the McArthur River unconformity-related U deposit include U, radiogenic Pb, V, Ni, Co, Cu, Mo, As, Zn, and rare earth elements. In this study, the mineralogical and paragenetic context for their occurrence was established by integrating in situ mineral chemistry and laser ablation mass spectrometry chemical mapping of interstitial assemblages, detrital grains, and cements with whole-rock analyses of drill core samples from the diagenetically altered background and the hydrothermally altered sandstone host rocks. Diagenetically altered background sandstones contain a matrix assemblage of illite and dickite, with trace to minor aluminum-phosphate-sulfate (APS) minerals, apatite, and Fe-Ti oxide minerals. Aluminum-phosphate-sulfate minerals account for the majority of the Sr and light rare earth element concentrations, whereas early diagenetic apatite, monazite, and apatite inclusions in detrital quartz and detrital zircon contribute significant U and heavy rare earth elements to samples analyzed with an aggressive leach (partial digestion) such as aqua regia. Hydrothermally altered sandstone host rocks also contain variable assemblages of Al-Mg chlorite (sudoite), alkali-deficient tourmaline, APS minerals, kaolinite, illite, Fe-oxide, and sulfide minerals. Late pre-mineralization chlorite accounts for a significant portion of the observed Ni concentrations, whereas Co, Cu, Mo, and Zn occur predominantly in cryptic sub-micron sulfide and sulfarsenide inclusions within clay mineral aggregates and in association with Fe-Ti oxides. Elevated concentrations of U were observed in cryptic micro-inclusions associated with sulfides in quartz overgrowths, with Fe-Ti oxide micro-inclusions in kaolinite, and in post-mineralization Fe-oxide veins. The distribution of pathfinder elements throughout the deposit footprint appears to be less related to the primary dispersion of alteration minerals from the hydrothermal system than to the secondary dispersion of elements post-mineralization. Their occurrence throughout pre-, syn-, and post-mineralization assemblages further demonstrates the limitations to defining geochemical footprints from pathfinder element concentrations expressed in lithogeochemical data sets without structural, lithological, and mineralogical context.

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38

Warman, Emily A., Shivani S. Singh, Alicia G. Gubieda, and David C. Grainger. "A non-canonical promoter element drives spurious transcription of horizontally acquired bacterial genes." Nucleic Acids Research 48, no. 9 (April 16, 2020): 4891–901. http://dx.doi.org/10.1093/nar/gkaa244.

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Abstract RNA polymerases initiate transcription at DNA sequences called promoters. In bacteria, the best conserved promoter feature is the AT-rich -10 element; a sequence essential for DNA unwinding. Further elements, and gene regulatory proteins, are needed to recruit RNA polymerase to the -10 sequence. Hence, -10 elements cannot function in isolation. Many horizontally acquired genes also have a high AT-content. Consequently, sequences that resemble the -10 element occur frequently. As a result, foreign genes are predisposed to spurious transcription. However, it is not clear how RNA polymerase initially recognizes such sequences. Here, we identify a non-canonical promoter element that plays a key role. The sequence, itself a short AT-tract, resides 5 base pairs upstream of otherwise cryptic -10 elements. The AT-tract alters DNA conformation and enhances contacts between the DNA backbone and RNA polymerase.

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39

Dabrowski, Patrice M. "Folk, Faith and Fatherland: Defining the Polish Nation in 1883." Nationalities Papers 28, no. 3 (September 2000): 397–416. http://dx.doi.org/10.1080/713687474.

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On the north wall of Cracow's Church of the Annunciation (better known as the Carmelite Church at Piaski) hangs a long-ignored inscription. A simple stone tablet unprotected from the elements, its words have faded over the past century. One must strain to make out its cryptic message: “On September 11, 1883, Polish villagers gathered in Cracow solemnly celebrated the two hundredth anniversary of the relief of Vienna by John Sobieski, in remembrance of which this stone has been funded.”

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40

McCauley, Brenna, Luyang Sun, and Weiwei Dang. "CRYPTIC TRANSCRIPTION IS ASSOCIATED WITH AGE IN MAMMALIAN STEM CELLS." Innovation in Aging 3, Supplement_1 (November 2019): S963. http://dx.doi.org/10.1093/geroni/igz038.3493.

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Abstract Aging is a multifaceted process that challenges organisms with stresses resulting from the dysregulation of cellular processes. Unsurprisingly, given how tightly regulated it is under normal conditions, transcription is one of the key pathways disrupted during aging. Indeed, dysregulation of transcription contributes to the activation of transposable elements, the loss of cellular identity, and decreased stem cell potency with age. Our previous work identified intragenic cryptic transcription (CT) as a novel type of age-associated transcriptional dysregulation that limits the lifespan of yeast and worms. Continuing this work, we show for the first time that CT increases with age in mammalian stem cells. Increased CT is associated with disrupted chromatin structure, particularly with the reduction of H3K36me3, a histone modification known to inhibit CT throughout eukaryotes. We propose that an age-associated reduction in H3K36me3 in actively transcribed gene bodies drives disruption of chromatin structure in these regions, resulting in an open chromatin state. This open chromatin state is permissive for the entry of RNA Pol II, which can then initiate transcription from within the gene body. These aberrant cryptic transcripts may contribute to the pathological load of mammalian aging.

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41

Moles-Fernández, Alejandro, Joanna Domènech-Vivó, Anna Tenés, Judith Balmaña, Orland Diez, and Sara Gutiérrez-Enríquez. "Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes." Cancers 13, no. 13 (July 3, 2021): 3341. http://dx.doi.org/10.3390/cancers13133341.

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The contribution of deep intronic splice-altering variants to hereditary breast and ovarian cancer (HBOC) is unknown. Current computational in silico tools to predict spliceogenic variants leading to pseudoexons have limited efficiency. We assessed the performance of the SpliceAI tool combined with ESRseq scores to identify spliceogenic deep intronic variants by affecting cryptic sites or splicing regulatory elements (SREs) using literature and experimental datasets. Our results with 233 published deep intronic variants showed that SpliceAI, with a 0.05 threshold, predicts spliceogenic deep intronic variants affecting cryptic splice sites, but is less effective in detecting those affecting SREs. Next, we characterized the SRE profiles using ESRseq, showing that pseudoexons are significantly enriched in SRE-enhancers compared to adjacent intronic regions. Although the combination of SpliceAI with ESRseq scores (considering ∆ESRseq and SRE landscape) showed higher sensitivity, the global performance did not improve because of the higher number of false positives. The combination of both tools was tested in a tumor RNA dataset with 207 intronic variants disrupting splicing, showing a sensitivity of 86%. Following the pipeline, five spliceogenic deep intronic variants were experimentally identified from 33 variants in HBOC genes. Overall, our results provide a framework to detect deep intronic variants disrupting splicing.

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42

Thirunavukkarasu, Kannan, Rebecca R. Miles, David L. Halladay, and Jude E. Onyia. "Cryptic Enhancer Elements in Luciferase Reporter Vectors Respond to the Osteoblast-Specific Transcription Factor Osf2/Cbfa1." BioTechniques 28, no. 3 (March 2000): 506–10. http://dx.doi.org/10.2144/00283st09.

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43

Samuelson, L. C., K. Wiebauer, C. M. Snow, and M. H. Meisler. "Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution." Molecular and Cellular Biology 10, no. 6 (June 1990): 2513–20. http://dx.doi.org/10.1128/mcb.10.6.2513-2520.1990.

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We have analyzed the junction regions of inserted elements within the human amylase gene complex. This complex contains five genes which are expressed at high levels either in the pancreas or in the parotid gland. The proximal 5'-flanking regions of these genes contain two inserted elements. A gamma-actin pseudogene is located at a position 200 base pairs upstream of the first coding exon. All of the amylase genes contain this insert. The subsequent insertion of an endogenous retrovirus interrupted the gamma-actin pseudogene within its 3'-untranslated region. Nucleotide sequence analysis of the inserted elements associated with each of the five human amylase genes has revealed a series of molecular events during the recent history of this gene family. The data indicate that the entire gene family was generated during primate evolution from one ancestral gene copy and that the retroviral insertion activated a cryptic promoter.

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44

Samuelson, L. C., K. Wiebauer, C. M. Snow, and M. H. Meisler. "Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution." Molecular and Cellular Biology 10, no. 6 (June 1990): 2513–20. http://dx.doi.org/10.1128/mcb.10.6.2513.

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Анотація:

We have analyzed the junction regions of inserted elements within the human amylase gene complex. This complex contains five genes which are expressed at high levels either in the pancreas or in the parotid gland. The proximal 5'-flanking regions of these genes contain two inserted elements. A gamma-actin pseudogene is located at a position 200 base pairs upstream of the first coding exon. All of the amylase genes contain this insert. The subsequent insertion of an endogenous retrovirus interrupted the gamma-actin pseudogene within its 3'-untranslated region. Nucleotide sequence analysis of the inserted elements associated with each of the five human amylase genes has revealed a series of molecular events during the recent history of this gene family. The data indicate that the entire gene family was generated during primate evolution from one ancestral gene copy and that the retroviral insertion activated a cryptic promoter.

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45

Nakashima, Nobutaka, and Tomohiro Tamura. "Isolation and Characterization of a Rolling-Circle-Type Plasmid from Rhodococcus erythropolis and Application of the Plasmid to Multiple-Recombinant-Protein Expression." Applied and Environmental Microbiology 70, no. 9 (September 2004): 5557–68. http://dx.doi.org/10.1128/aem.70.9.5557-5568.2004.

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ABSTRACT We isolated, sequenced, and characterized the cryptic plasmid pRE8424 from Rhodococcus erythropolis DSM8424. Plasmid pRE8424 is a 5,987-bp circular plasmid; it carries six open reading frames and also contains cis-acting elements, specifically a single-stranded origin and a double-stranded origin, which are characteristic of rolling-circle-replication plasmids. Experiments with pRE8424 derivatives carrying a mutated single-stranded origin sequence showed that single-stranded DNA intermediates accumulated in the cells because of inefficient conversion from single-stranded DNA to double-stranded DNA. This result indicates that pRE8424 belongs to the pIJ101/pJV1 family of rolling-circle-replication plasmids. Expression vectors that are functional in several Rhodococcus species were constructed by use of the replication origin from pRE8424. We previously reported a cryptic plasmid, pRE2895, from R. erythropolis, which may replicate by a θ-type mechanism, like ColE2 plasmids. The new expression vectors originating from pRE8424 were compatible with those derived from pRE2895. Coexpression experiments with these compatible expression vectors indicated that the plasmids are suitable for the simultaneous expression of multiple recombinant proteins.

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46

Handford, Cynthia L., Charma T. Stang, Tracy L. Raivio, and Jonathan J. Dennis. "The contribution of small cryptic plasmids to the antibiotic resistance of enteropathogenic Escherichia coli E2348/69." Canadian Journal of Microbiology 55, no. 11 (November 2009): 1229–39. http://dx.doi.org/10.1139/w09-079.

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Two uncharacterized small cryptic plasmids (SCPs) were isolated from enteropathogenic Escherichia coli strain E2348/69. Genomic DNA sequence analysis of both SCPs indicated that the smaller plasmid, p5217, encoded several mobilization genes, whereas the larger plasmid, p6148, encoded several putative antibiotic resistance determinants. Complementation analysis showed that p6148 encodes functional streptomycin resistance genes but, owing to the presence of several frameshift mutations, a nonfunctional sulfonamide resistance determinant. A plasmid similar to p6148 has previously been shown to confer a slight growth advantage on E. coli. However, we were unable to observe any significant growth advantage in different E. coli strains transformed with p6148. The p6148 DNA sequence is homologous in sequence and arrangement to DNA from other plasmid families, including large conjugative plasmids and SXT integrative and conjugative elements. This study suggests that gene clusters of the sul2–strAB antibiotic resistance genes are widespread and highly transferable, owing to their presence in a wide variety of mobile genetic elements.

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47

Jang, Woori, Joonhong Park, Hyojin Chae, and Myungshin Kim. "Comparison of In Silico Tools for Splice-Altering Variant Prediction Using Established Spliceogenic Variants: An End-User’s Point of View." International Journal of Genomics 2022 (October 13, 2022): 1–6. http://dx.doi.org/10.1155/2022/5265686.

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Assessing the impact of variants of unknown significance on splicing has become a critical issue and a bottleneck, especially with the widespread implementation of whole-genome or exome sequencing. Although multiple in silico tools are available, the interpretation and application of these tools are difficult and practical guidelines are still lacking. A streamlined decision-making process can facilitate the downstream RNA analysis in a more efficient manner. Therefore, we evaluated the performance of 8 in silico tools (Splice Site Finder, MaxEntScan, Splice-site prediction by neural network, GeneSplicer, Human Splicing Finder, SpliceAI, Splicing Predictions in Consensus Elements, and SpliceRover) using 114 NF1 spliceogenic variants, experimentally validated at the mRNA level. The change in the predicted score incurred by the variant of the nearest wild-type splice site was analyzed, and for type II, III, and IV splice variants, the change in the prediction score of de novo or cryptic splice site was also analyzed. SpliceAI and SpliceRover, tools based on deep learning, outperformed all other tools, with AUCs of 0.972 and 0.924, respectively. For de novo and cryptic splice sites, SpliceAI outperformed all other tools and showed a sensitivity of 95.7% at an optimal cut-off of 0.02 score change. Our results show that deep learning algorithms, especially those of SpliceAI, are validated at a significantly higher rate than other in silico tools for clinically relevant NF1 variants. This suggests that deep learning algorithms outperform traditional probabilistic approaches and classical machine learning tools in predicting the de novo and cryptic splice sites.

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48

Starostin, I. A., M. M. Girfanov, and E. I. Yartsev. "Geological features, hydrothermal alterations, and cryptic mineralogical zonation of the Kyzyk-Chadr porphyry copper deposit (Tyva Republic)." Moscow University Bulletin. Series 4. Geology, no. 5 (December 17, 2022): 90–94. http://dx.doi.org/10.33623/0579-9406-2022-5-78-89.

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The altered rocks of the Kyzyk-Cha dr deposit are predominantly composed of quartz and potassic dioctahedral micas of the phengite–muscovite series, that dominate in almost all zones of the alteration halo. Parageneses of albite with chlorite and epidote are only characteristic of peripheral sections of the halo, subjected to the propylite-type alteration. Quartz-potassium feldspar alterations are distributed in the central and deep-seated sections of the halo. Petrographic investigations of hydrothermal alterations and results of the X-ray structural analysis and infrared (IR) spectroscopy of micas from the mineralized quartz-sericite metasomatites were applied to reveal a cryptic mineralogical zonation of the Kyzyk-Chadr porphyry copper deposit. Elements of the cryptic mineralogical zonation, revealed based on results of the X-ray study and IR spectroscopy of light-colored micaceous metasomatites of the deposit, are caused by variable proportions of the phengite and muscovite components in their composition. The phengite component predominates in the central and deep-seated sections of the alteration-mineralization halo of the deposit, while the muscovite component progressively increases toward its flanks and upper sections. This tendency correlates with the general vector of the mineralogical alteration-mineralization zonation and are supposedly explained by changing PT conditions within the porphyry copper ore-magmatic system. The indicator of the cryptic mineralogical zonation by the “phengite-muscovite” relationship can be applied for prospecting and preliminary evaluation of porphyry copper type deposits, being used as an objective guide for correlation of already obtained ore-grade interceptions and forecasting the ore bodies.

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49

WILLIAMS, SUSAN M., LAUREN T. MACNAB, and DAVID V. POW. "Cryptic expression of functional glutamate transporters in the developing rodent brain." Neuron Glia Biology 2, no. 3 (August 2006): 199–215. http://dx.doi.org/10.1017/s1740925x06000263.

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The co-ordinate functioning of neurons and glia is required for glutamate-mediated neurotransmission. In this study, we show by immunocytochemical detection of D-aspartate uptake, that functional glutamate transporters are present in the developing CNS of fetal and neonatal rats, including forebrain, midbrain and hindbrain, at least as early as embryonic day 12 (E12). Use of the transport inhibitor dihydrokainic acid revealed a significant role for GLT-1 in the uptake process. Immunolabelling for the glutamate transporters GLAST, GLT-1α and GLT-1v showed that each of these proteins are expressed early in development and appear to be restricted to glial-like cells throughout the development period examined (except in the retina, where neuronal elements were also labelled). Our capacity to detect very early expression of the variant forms of GLT-1 contrasts with other studies, a feature that we attribute to the use of antigen-recovery techniques that unmask protein epitopes that are otherwise undetectable. These studies illustrate the widespread presence of functional glutamate transporters in the developing CNS, in many cases before the onset of periods of synaptogenesis and indicate that regulation of extracellular glutamate by multiple excitatory amino acid transporters might be crucial in early CNS development.

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50

Curry, John D., Danae Schulz, Cynthia J. Guidos, Jayne S. Danska, Lauryl Nutter, Andre Nussenzweig, and Mark S. Schlissel. "Chromosomal reinsertion of broken RSS ends during T cell development." Journal of Experimental Medicine 204, no. 10 (September 4, 2007): 2293–303. http://dx.doi.org/10.1084/jem.20070583.

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The V(D)J recombinase catalyzes DNA transposition and translocation both in vitro and in vivo. Because lymphoid malignancies contain chromosomal translocations involving antigen receptor and protooncogene loci, it is critical to understand the types of “mistakes” made by the recombinase. Using a newly devised assay, we characterized 48 unique TCRβ recombination signal sequence (RSS) end insertions in murine thymocyte and splenocyte genomic DNA samples. Nearly half of these events targeted “cryptic” RSS-like elements. In no instance did we detect target-site duplications, which is a hallmark of recombinase-mediated transposition in vitro. Rather, these insertions were most likely caused by either V(D)J recombination between a bona fide RSS and a cryptic RSS or the insertion of signal circles into chromosomal loci via a V(D)J recombination-like mechanism. Although wild-type, p53, p53 x scid, H2Ax, and ATM mutant thymocytes all showed similar levels of RSS end insertions, core-RAG2 mutant thymocytes showed a sevenfold greater frequency of such events. Thus, the noncore domain of RAG2 serves to limit the extent to which the integrity of the genome is threatened by mistargeting of V(D)J recombination.

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