Recently, we and others have shown that mutations in TMPRSS3 were responsible for autosomal reces... more Recently, we and others have shown that mutations in TMPRSS3 were responsible for autosomal recessive non-syndromic hearing loss. TMPRSS3 is a member of the Type II Transmembrane Serine Protease (TTSP) family and encodes for a protease that also contains LDLRA (low-density lipoprotein receptor class A) and SRCR (scavenger receptor cysteine rich) domains. Fourteen pathogenic mutations, which occur not only in the catalytic domain but also in the LDLRA and SRCR domains, have been identified to date that cause the DFNB8/10 forms of deafness. In vitro experiments demonstrated that TMPRSS3 mutants were proteolytically inactive indicating that TMPRSS3 protease activity is critical for normal auditory function. However, how missense mutations in the LDLRA and SRCR domains affect the proteolytic activity of TMPRSS3 remains to be elucidated. Although the role of TMPRSS3 in the auditory system is currently not completely understood, it has been shown to regulate the activity of the ENaC sodium channel in vitro and could therefore participate in the regulation of sodium concentration in the cochlea. TMPRSS3 mutations are not a common cause of hereditary deafness, the elucidation of its function is nevertheless important for better understanding of hearing, and provide biological targets for therapeutic interventions.
SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene e... more SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1], [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense tr...
... Page 12. 426 Stylianos E. Antonarakis and Hamish S. Scott 3. CM Fraser, JD Gocayne, O. White,... more ... Page 12. 426 Stylianos E. Antonarakis and Hamish S. Scott 3. CM Fraser, JD Gocayne, O. White, MD Adams, RA Clayton, RD Fleischmann, CJ Bult, AR Kerlavage, G. Sutton, JM Kelley, et al. (1995) The minimal gene complement of Mycoplasma genitaUum. ...
Following their generation in the germinal zones, young neurons of the neocortex, hippocampus and... more Following their generation in the germinal zones, young neurons of the neocortex, hippocampus and cerebellum undergo long-distance migration to reach their final destinations. This locomotive activity depends on active deployment of cytoskeletal elements including the microtubule apparatus. In this study, we report the identification and expression of radial spoke protein 3 (RSP3), a member of a protein cluster responsible for anchoring and modifying dynein motor activity known to be crucial to microtubule sliding. The mouse RSP3 gene consists of eight exons and seven introns and spans over 230 kb. The genomic organisations of the human and rat RSP3 genes are similar although they span approximately 23 and 53 kb, respectively. This is in contrast to the Chlamydomonas RSP3 gene, where RSP3 was first isolated, which consists of four exons and three introns and spans approximately 2.7 kb. Despite these differences, the nucleotide and amino acid sequences upstream of, and throughout the RPII-binding domain of RSP3 are highly conserved between all the above-mentioned species. Mouse RSP3 mRNA was restricted to the developing neocortex, hippocampus and cerebellum during the stages when these structures are known to contain large numbers of migratory neurons. Gene expression studies suggest that RSP3 function is consistent with a locomotory role for this protein in migrating young neurons. In addition, expression of RSP3 mRNA in adult neurons point to additional, though still unknown functions. Our data provides the first evidence for the expression of radial spoke proteins in higher eukaryotes, and provides a biological framework for how these proteins may participate in microtubule sliding and neuronal migration in the embryonic brain. D
Vinclozolin is an endocrine-disrupting chemical (EDC) that binds with high affinity to the androg... more Vinclozolin is an endocrine-disrupting chemical (EDC) that binds with high affinity to the androgen receptor (AR) and blocks the action of gonadal hormones on male reproductive organs. An alternative mechanism of action of Vinclozolin involves transgenerational effects on the male reproductive tract. We previously reported in utero Vinclozolin exposure-induced prostatitis (prostate inflammation) in postpubertal rats concurrent with down-regulation of AR and increased nuclear factor-kappaB activation. We postulated the male reproductive abnormalities induced by in utero Vinclozolin exposure could be reversed by testosterone supplementation, in contrast to the permanent modifications involving DNA methyltransferases (Dnmts) described by others. To test this hypothesis, we administered high-dose testosterone at puberty to Vinclozolin-treated rats and determined the effect on anogenital distance (AGD); testicular germ cell apoptosis, concentration of elongated spermatids, and the onset of prostatitis. Concurrently we examined Dnmt1, -3A, -3B, and -3L mRNA expression. Consistent with previous reports, in utero exposure to Vinclozolin significantly reduced AGD, increased testicular germ cell apoptosis 3-fold, reduced elongated spermatid number by 40%, and induced postpubertal prostatitis in 100% of exposed males. Administration of high-dose testosterone (25 mg/kg) at puberty normalized AGD, reduced germ cell apoptosis, and restored elongated spermatid number. Testosterone restored AR and nuclear factor-kappaB expression in the prostate and abolished Vinclozolin-induced prostatitis. Altered Dnmt expression was evident with in utero Vinclozolin exposure and was not normalized after testosterone treatment. These data demonstrate in utero Vinclozolin-induced male reproductive tract abnormalities are AR mediated and reversible and involve a mechanism independent of Dnmt expression.
Please cite this article as: Mordaunt D, Oftedal BE, McLauchlan A, Coates D, Waters W, Scott H, B... more Please cite this article as: Mordaunt D, Oftedal BE, McLauchlan A, Coates D, Waters W, Scott H, Barnett C, 8q13.1-q13.2 deletion associated with inferior cerebellar vermian hypoplasia and digital anomalies: a new syndrome, Pediatric Neurology (2014), Title: 8q13.1-q13.2 deletion associated with inferior cerebellar vermian hypoplasia and digital anomalies: a new syndrome. (116 characters)
Atypical chronic myeloid leukemia (aCML) is a rare leukemic disorder with no specific genetic les... more Atypical chronic myeloid leukemia (aCML) is a rare leukemic disorder with no specific genetic lesion. Here we demonstrate clonal occurrences of tetrasomy for the long arm of chromosome 21 in a patient with aCML, and a thorough review of the literature provides evidence that this chromosomal anomaly is a so far not recognised recurrent finding in aCML. Further, the timely association of the occurrence of the tetrasomy 21q with acceleration of the leukemia suggests a role for chromosome 21 in leukemic disease progression. The chromosome 21 gene most strongly implicated in both normal and abnormal hematopoiesis is RUNX1. Also, RUNX1 haploinsufficiency due to RUNX1 point mutations characterises the familial platelet disorder with propensity to develop leukemia, and thromboytopenia was a leading feature in the present case. Therefore, an extensive molecular analysis of RUNX1 was performed. However, these analyses did not reveal a mutation, and the results support a gene dosage effect for RUNX1 in myeloid disease similar to observations in lymphoid disease. Patients with aCML and a tetrasomy 21 may form a karyotypically and phenotypically defined subgroup of aCML.
Trisomy 21, which causes Down syndrome, is the model human disorder due to the presence of a supe... more Trisomy 21, which causes Down syndrome, is the model human disorder due to the presence of a supernumerary chromosome. The completion of the sequence of chromosome 21 and the development of appropriate animal models now provide the molecular infrastructure and the reagents to elucidate the molecular mechanisms of the different phenotypes of Down syndrome. The study of the overexpression of single genes, and the dysregulation of global gene expression will enhance the understanding of the pathogenesis of the cognitive impairment of this syndrome.
piRNAs are critical for transposable element (TE) repression and germ cell survival during the ea... more piRNAs are critical for transposable element (TE) repression and germ cell survival during the early phases of spermatogenesis, however, their role in adult germ cells and the relative importance of piRNA methylation is poorly defined in mammals. Using a mouse model of HEN methyltransferase 1 (HENMT1) loss-of-function, RNA-Seq and a range of RNA assays we show that HENMT1 is required for the 2' O-methylation of mammalian piRNAs. HENMT1 loss leads to piRNA instability, reduced piRNA bulk and length, and ultimately male sterility characterized by a germ cell arrest at the elongating germ cell phase of spermatogenesis. HENMT1 loss-of-function, and the concomitant loss of piRNAs, resulted in TE de-repression in adult meiotic and haploid germ cells, and the precocious, and selective, expression of many haploid-transcripts in meiotic cells. Precocious expression was associated with a more active chromatin state in meiotic cells, elevated levels of DNA damage and a catastrophic deregul...
Biological and biomedical research relies on comprehensive understanding of protein-coding transc... more Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like ...
We have recently cloned four novel human genes that encode the ancient conserved domain proteins ... more We have recently cloned four novel human genes that encode the ancient conserved domain proteins (ACDP). The full-length cDNA sequence of ACDP1 consists of 5898 bp and encodes a predicted protein of 951 amino acids (AA). The transcript for ACDP2 has 4058 bp of cDNA sequence, encoding a protein of 875 AA. ACDP3 contains 3113 bp of cDNA sequence and
Proceedings of the National Academy of Sciences of the United States of America, Jan 20, 2015
Hepatitis B virus (HBV) infection can result in a spectrum of outcomes from immune-mediated contr... more Hepatitis B virus (HBV) infection can result in a spectrum of outcomes from immune-mediated control to disease progression, cirrhosis, and liver cancer. The host molecular pathways that influence and contribute to these outcomes need to be defined. Using an immunocompetent mouse model of chronic HBV infection, we identified some of the host cellular and molecular factors that impact on infection outcomes. Here, we show that cellular inhibitor of apoptosis proteins (cIAPs) attenuate TNF signaling during hepatitis B infection, and they restrict the death of infected hepatocytes, thus allowing viral persistence. Animals with a liver-specific cIAP1 and total cIAP2 deficiency efficiently control HBV infection compared with WT mice. This phenotype was partly recapitulated in mice that were deficient in cIAP2 alone. These results indicate that antagonizing the function of cIAPs may promote the clearance of HBV infection.
Recently, we and others have shown that mutations in TMPRSS3 were responsible for autosomal reces... more Recently, we and others have shown that mutations in TMPRSS3 were responsible for autosomal recessive non-syndromic hearing loss. TMPRSS3 is a member of the Type II Transmembrane Serine Protease (TTSP) family and encodes for a protease that also contains LDLRA (low-density lipoprotein receptor class A) and SRCR (scavenger receptor cysteine rich) domains. Fourteen pathogenic mutations, which occur not only in the catalytic domain but also in the LDLRA and SRCR domains, have been identified to date that cause the DFNB8/10 forms of deafness. In vitro experiments demonstrated that TMPRSS3 mutants were proteolytically inactive indicating that TMPRSS3 protease activity is critical for normal auditory function. However, how missense mutations in the LDLRA and SRCR domains affect the proteolytic activity of TMPRSS3 remains to be elucidated. Although the role of TMPRSS3 in the auditory system is currently not completely understood, it has been shown to regulate the activity of the ENaC sodium channel in vitro and could therefore participate in the regulation of sodium concentration in the cochlea. TMPRSS3 mutations are not a common cause of hereditary deafness, the elucidation of its function is nevertheless important for better understanding of hearing, and provide biological targets for therapeutic interventions.
SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene e... more SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1], [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense tr...
... Page 12. 426 Stylianos E. Antonarakis and Hamish S. Scott 3. CM Fraser, JD Gocayne, O. White,... more ... Page 12. 426 Stylianos E. Antonarakis and Hamish S. Scott 3. CM Fraser, JD Gocayne, O. White, MD Adams, RA Clayton, RD Fleischmann, CJ Bult, AR Kerlavage, G. Sutton, JM Kelley, et al. (1995) The minimal gene complement of Mycoplasma genitaUum. ...
Following their generation in the germinal zones, young neurons of the neocortex, hippocampus and... more Following their generation in the germinal zones, young neurons of the neocortex, hippocampus and cerebellum undergo long-distance migration to reach their final destinations. This locomotive activity depends on active deployment of cytoskeletal elements including the microtubule apparatus. In this study, we report the identification and expression of radial spoke protein 3 (RSP3), a member of a protein cluster responsible for anchoring and modifying dynein motor activity known to be crucial to microtubule sliding. The mouse RSP3 gene consists of eight exons and seven introns and spans over 230 kb. The genomic organisations of the human and rat RSP3 genes are similar although they span approximately 23 and 53 kb, respectively. This is in contrast to the Chlamydomonas RSP3 gene, where RSP3 was first isolated, which consists of four exons and three introns and spans approximately 2.7 kb. Despite these differences, the nucleotide and amino acid sequences upstream of, and throughout the RPII-binding domain of RSP3 are highly conserved between all the above-mentioned species. Mouse RSP3 mRNA was restricted to the developing neocortex, hippocampus and cerebellum during the stages when these structures are known to contain large numbers of migratory neurons. Gene expression studies suggest that RSP3 function is consistent with a locomotory role for this protein in migrating young neurons. In addition, expression of RSP3 mRNA in adult neurons point to additional, though still unknown functions. Our data provides the first evidence for the expression of radial spoke proteins in higher eukaryotes, and provides a biological framework for how these proteins may participate in microtubule sliding and neuronal migration in the embryonic brain. D
Vinclozolin is an endocrine-disrupting chemical (EDC) that binds with high affinity to the androg... more Vinclozolin is an endocrine-disrupting chemical (EDC) that binds with high affinity to the androgen receptor (AR) and blocks the action of gonadal hormones on male reproductive organs. An alternative mechanism of action of Vinclozolin involves transgenerational effects on the male reproductive tract. We previously reported in utero Vinclozolin exposure-induced prostatitis (prostate inflammation) in postpubertal rats concurrent with down-regulation of AR and increased nuclear factor-kappaB activation. We postulated the male reproductive abnormalities induced by in utero Vinclozolin exposure could be reversed by testosterone supplementation, in contrast to the permanent modifications involving DNA methyltransferases (Dnmts) described by others. To test this hypothesis, we administered high-dose testosterone at puberty to Vinclozolin-treated rats and determined the effect on anogenital distance (AGD); testicular germ cell apoptosis, concentration of elongated spermatids, and the onset of prostatitis. Concurrently we examined Dnmt1, -3A, -3B, and -3L mRNA expression. Consistent with previous reports, in utero exposure to Vinclozolin significantly reduced AGD, increased testicular germ cell apoptosis 3-fold, reduced elongated spermatid number by 40%, and induced postpubertal prostatitis in 100% of exposed males. Administration of high-dose testosterone (25 mg/kg) at puberty normalized AGD, reduced germ cell apoptosis, and restored elongated spermatid number. Testosterone restored AR and nuclear factor-kappaB expression in the prostate and abolished Vinclozolin-induced prostatitis. Altered Dnmt expression was evident with in utero Vinclozolin exposure and was not normalized after testosterone treatment. These data demonstrate in utero Vinclozolin-induced male reproductive tract abnormalities are AR mediated and reversible and involve a mechanism independent of Dnmt expression.
Please cite this article as: Mordaunt D, Oftedal BE, McLauchlan A, Coates D, Waters W, Scott H, B... more Please cite this article as: Mordaunt D, Oftedal BE, McLauchlan A, Coates D, Waters W, Scott H, Barnett C, 8q13.1-q13.2 deletion associated with inferior cerebellar vermian hypoplasia and digital anomalies: a new syndrome, Pediatric Neurology (2014), Title: 8q13.1-q13.2 deletion associated with inferior cerebellar vermian hypoplasia and digital anomalies: a new syndrome. (116 characters)
Atypical chronic myeloid leukemia (aCML) is a rare leukemic disorder with no specific genetic les... more Atypical chronic myeloid leukemia (aCML) is a rare leukemic disorder with no specific genetic lesion. Here we demonstrate clonal occurrences of tetrasomy for the long arm of chromosome 21 in a patient with aCML, and a thorough review of the literature provides evidence that this chromosomal anomaly is a so far not recognised recurrent finding in aCML. Further, the timely association of the occurrence of the tetrasomy 21q with acceleration of the leukemia suggests a role for chromosome 21 in leukemic disease progression. The chromosome 21 gene most strongly implicated in both normal and abnormal hematopoiesis is RUNX1. Also, RUNX1 haploinsufficiency due to RUNX1 point mutations characterises the familial platelet disorder with propensity to develop leukemia, and thromboytopenia was a leading feature in the present case. Therefore, an extensive molecular analysis of RUNX1 was performed. However, these analyses did not reveal a mutation, and the results support a gene dosage effect for RUNX1 in myeloid disease similar to observations in lymphoid disease. Patients with aCML and a tetrasomy 21 may form a karyotypically and phenotypically defined subgroup of aCML.
Trisomy 21, which causes Down syndrome, is the model human disorder due to the presence of a supe... more Trisomy 21, which causes Down syndrome, is the model human disorder due to the presence of a supernumerary chromosome. The completion of the sequence of chromosome 21 and the development of appropriate animal models now provide the molecular infrastructure and the reagents to elucidate the molecular mechanisms of the different phenotypes of Down syndrome. The study of the overexpression of single genes, and the dysregulation of global gene expression will enhance the understanding of the pathogenesis of the cognitive impairment of this syndrome.
piRNAs are critical for transposable element (TE) repression and germ cell survival during the ea... more piRNAs are critical for transposable element (TE) repression and germ cell survival during the early phases of spermatogenesis, however, their role in adult germ cells and the relative importance of piRNA methylation is poorly defined in mammals. Using a mouse model of HEN methyltransferase 1 (HENMT1) loss-of-function, RNA-Seq and a range of RNA assays we show that HENMT1 is required for the 2' O-methylation of mammalian piRNAs. HENMT1 loss leads to piRNA instability, reduced piRNA bulk and length, and ultimately male sterility characterized by a germ cell arrest at the elongating germ cell phase of spermatogenesis. HENMT1 loss-of-function, and the concomitant loss of piRNAs, resulted in TE de-repression in adult meiotic and haploid germ cells, and the precocious, and selective, expression of many haploid-transcripts in meiotic cells. Precocious expression was associated with a more active chromatin state in meiotic cells, elevated levels of DNA damage and a catastrophic deregul...
Biological and biomedical research relies on comprehensive understanding of protein-coding transc... more Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like ...
We have recently cloned four novel human genes that encode the ancient conserved domain proteins ... more We have recently cloned four novel human genes that encode the ancient conserved domain proteins (ACDP). The full-length cDNA sequence of ACDP1 consists of 5898 bp and encodes a predicted protein of 951 amino acids (AA). The transcript for ACDP2 has 4058 bp of cDNA sequence, encoding a protein of 875 AA. ACDP3 contains 3113 bp of cDNA sequence and
Proceedings of the National Academy of Sciences of the United States of America, Jan 20, 2015
Hepatitis B virus (HBV) infection can result in a spectrum of outcomes from immune-mediated contr... more Hepatitis B virus (HBV) infection can result in a spectrum of outcomes from immune-mediated control to disease progression, cirrhosis, and liver cancer. The host molecular pathways that influence and contribute to these outcomes need to be defined. Using an immunocompetent mouse model of chronic HBV infection, we identified some of the host cellular and molecular factors that impact on infection outcomes. Here, we show that cellular inhibitor of apoptosis proteins (cIAPs) attenuate TNF signaling during hepatitis B infection, and they restrict the death of infected hepatocytes, thus allowing viral persistence. Animals with a liver-specific cIAP1 and total cIAP2 deficiency efficiently control HBV infection compared with WT mice. This phenotype was partly recapitulated in mice that were deficient in cIAP2 alone. These results indicate that antagonizing the function of cIAPs may promote the clearance of HBV infection.
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