Biomedical subjects

Nabeel A Affara

Publications and source records attributed to Nabeel A Affara.

8 recordsLinked to original sources

PubMed2005

Deletions on mouse Yq lead to upregulation of multiple X- and Y-linked transcripts in spermatids.

Deletions on the mouse Y-chromosome long arm (MSYq) lead to teratozoospermia and in severe cases to infertility. We find that the downstream transcriptional changes in the testis resulting from the loss of MSYq-encoded transcripts involve upregulation of multiple X- and Y-linked spermatid-expressed genes, but not related autosomal genes. Therefore, this indicates that in normal males, there is a specific repression of X and Y (gonosomal) transcription in post-meiotic cells, which depends on MSYq-encoded transcripts. Together with the known sex ratio skew in favour of females in the offspring of fertile MSYqdel males, this strongly suggests the existence of an intragenomic conflict between X- and Y-linked genes. Two potential antagonists in this conflict are the X-linked multicopy gene Xmr and its multicopy MSYq-linked relative Sly, which are upregulated and downregulated, respectively, in the testes of MSYqdel males. Xmr is also expressed during meiotic sex chromosome inactivation (MSCI), indicating a link between the MSCI and the MSYq-dependent gonosomal repression in spermatids. We therefore propose that this repression and MSCI itself are evolutionary adaptations to maintain a normal sex ratio in the face of X/Y antagonism.

Adaptor Proteins, Signal Transducing↗

PubMed2004

Sperm-induced modification of the oviductal gene expression profile after natural insemination in mice.

In mammals, the physiological interaction between spermatozoa and oviductal epithelia involves intimate and specific contact between the two cell types. Spermatozoa may undergo stringent selection processes within the female reproductive tract before they meet and fertilize oocytes. The physiological basis of the sperm selection process is largely unknown. Here we tested the hypothesis that the oviduct has a recognition system for spermatozoa that can detect the arrival of spermatozoa in the oviduct after insemination, resulting in alterations of the oviductal transcriptome. We initially performed a global screening of the oviductal transcriptome in mice 1) at the time of estrus (mating) and 2) 6 h after mating. Transcriptional alterations in the oviduct after mating were attributed to the presence of spermatozoa in the oviduct after mating and also to changes in the hormonal environment as female mice underwent the transition from estrus to diestrus. To distinguish these possibilities, female mice were then mated with T145H mutant mice, which because of spermatogenic arrest, produce seminal plasma but no spermatozoa. Focusing on two molecules that in the first experiment were upregulated after mating, it was found that adrenomedullin and prostaglandin endoperoxidase synthase 2 transcripts were upregulated in the oviducts of mice only after mating with fertile males; those mated with T145H infertile males showed significantly less response. These results indicate that it is the arrival of spermatozoa in the oviduct that activates one or more signal transduction pathways and leads to changes in the oviductal transcriptome profiles.

Adrenomedullin↗

PubMed2004

Protocadherin X ( PCDHX) and Y ( PCDHY) genes; multiple mRNA isoforms encoding variant signal peptides and cytoplasmic domains.

The gene-poor, hominid-specific Yp11.2/Xq21.3 X-Y homology block encodes two members of the protocadherin group of cell surface molecules, PCDHX and PCDHY. These two genes, mainly expressed in brain, were known to be composed of at least six exons sharing 98.1% DNA identity. The genomic structure of PCDHX/ Y has been reanalyzed in detail, uncovering the existence of at least 11 more exons spanning more than 700 kb. Many of these exons located at the 5' and 3' ends of PCDHX/ Y undergo differential and alternative splicing. Seven of the exons have been found to use alternative splice sites. Most of these variants are expressed within the brain, although some isoforms exhibit a more ubiquitous distribution pattern. PCDHX/ Y transcription appears to be driven from two alternative promoters located usptream of exon 1 and exon 4.1. Assuming that the splicing events at the 5' and 3' ends of these genes are independent of one another, potentially up to 360 different mRNAs could be produced. The main impact on protein function is predicted to be in the efficiency of translation, post-translational processing within the cell, and structure of the cytoplasmic domain that may influence any role the genes have in signaling.

Alternative Splicing↗

PubMed2004

A comparative analysis of the pig, mouse, and human PCDHX genes.

Protocadherin X and Y (PCDHX/Y) represent a pair of homologous genes located on the human sex chromosomes that are primarily expressed in the brain. PCDHY emerged as a result of a duplicative transposition from the X Chromosome (Chr) and is present on the Y only in hominids. Previous zoo-blot analysis suggested the existence of PCDHX orthologs on the X Chr of several mammalian species. This paper reports the cloning and characterization of porcine and murine Pcdhx. Pig Pcdhx cDNA was obtained by a combination of RT-PCR, SMART-RACE, and genomic sequencing and exhibits 88% identity to human PCDHX; FISH analysis indicated that porcine Pcdhx maps to Xq. Mouse Pcdhx cDNA was assembled by RT-PCR and database analysis and is 84% identical to the human gene. Some degree of alternative splicing was detected in pig Pcdhx, but not to the extent previously described in humans. Both murine and porcine Pcdhx mRNA were detected in all tissues studied. Cloning of 2.5 kb of genomic sequence upstream of the most 5' exon of porcine Pcdhx allowed a comparative analysis with murine and human sequences in order to define potential promoter elements. All exons present in mouse and pig transcripts were found to have homologous sequences in human DNA. Not all of these exons are represented in human transcripts, indicating differential evolution and usage. The increased complexity in post-transcriptional processing and restriction of expression of the human genes primarily to central nervous system tissue as compared with pig and mouse suggests that PCDHX/Y is potentially a good candidate to account for human-specific features of the CNS.

Amino Acid Sequence↗

PubMed2003

Usp9y (ubiquitin-specific protease 9 gene on the Y) is associated with a functional promoter and encodes an intact open reading frame homologous to Usp9x that is under selective constraint.

Sequences complementary to the X-linked ubiquitin-specific protease gene Usp9x (Dffrx) have been shown to map to the Sxr(b) interval of the mouse Y Chromosome (chr) and to be expressed in a testis-specific manner. In humans, ubiquitously expressed functional homologues (USP9Y and USP9X DFFRY/DFFRX) are present on both sex chromosomes, whereas in mouse it remains to be demonstrated that the Y-linked sequences encode a functional protein. In this paper, it is shown that the Usp9y gene encodes a potentially functional ubiquitin-specific protease possessing a core promoter region that shares several features characteristic of other testis-specific genes. Analysis of synonymous and nonsynonymous nucleotide changes suggests that there is constraint on the amino acid sequence of both the mouse Usp9x and Usp9y genes, a finding that mirrors similar analysis of the human orthologs. Thus, in both mouse and human, selection is acting to maintain the amino acid sequence of the X and Y-linked genes. This indicates that in both species the genes on each sex chromosome continue to encode an important function.

Amino Acid Sequence↗

PubMed2003

Resource and hardware options for microarray-based experimentation.

DNA microarray technology permits the study of biological systems and processes on a genome-wide scale. Arrays based on cDNA clones, oligonucleotides and genomic clones have been developed for investigations of gene expression, genetic analysis and genomic changes associated with disease. Over the past 3-4 years, microarrays have become more widely available to the research community. This has occurred through increased commercial availability of custom and generic arrays and the development of robotic equipment that has enabled array printing and analysis facilities to be established in academic research institutions. This brief review examines the public and commercial resources, the microarray fabrication and data capture and analysis equipment currently available to the user.

Computational Biology↗

PubMed2002

The human-specific Yp11.2/Xq21.3 homology block encodes a potentially functional testis-specific TGIF-like retroposon.

Yp11.2/Xq21.3 is a human-specific homology block that constitutes the largest shared region among the sex chromosomes, spanning some 3.5 Mb. Only two transcribed sequences have been mapped to this segment: the protocadherin genes PCDHX/Y, and the X-linked poly(A)-binding protein PABPC5 gene, whose Y-homolog has been lost during human evolution. This paper reports the genomic structure, expression, and evolutionary conservation of a third (X-Y homologous) transcribed sequence, TGIFLX/Y (TGIF-like X/Y), mapping to this region. TGIFLX/Y has a 2666-bp mRNA encoded by two exons separated by a 96-bp intron. TGIFLX/Y are homeodomain-containing genes related to the TALE superclass gene family. Comparative DNA analysis indicates that TGIFLX originated from retrotransposition of TGIF2, located on 20q11.2-12, onto the X Chromosome. RT-PCR analysis reveals that both X- and Y-linked genes are specifically expressed in adult testis. Cloning and sequencing of TGIFLX homologs in hominoids and Old World monkeys provides evidence for an open reading frame in the eight species studied. Interestingly, a single base pair deletion in the human TGIFLY (as compared with TGIFLX) creates a different reading frame where the C-terminal residues shared by TGIFLX and other TGIF proteins are missing. The conservation, similarity to protein-encoding transcription factors, and specific expression in testis points to a transcriptional role for TGIFLX/Y in this tissue.

Amino Acid Sequence↗

PubMed2002

A mapping and evolutionary study of porcine sex chromosome genes.

A combination of FISH and RH mapping was used to study the evolution of sex chromosome genes in the pig. In total, 19 genes were identified, including 3 PAR genes (STS, KAL, PRK). The gene order of the porcine X Chromosome (Chr) closely resembled the human X Chr (PRK/STS/KAL-AMELX-EIF2s3X/ZFX-USP9X-DBX-SMCX), suggesting that the porcine X has undergone very little rearrangement during evolution. For the porcine Y Chr, two linkage groups of 10 NRY genes were found, and the following order was established: Ypter-(AMELY-EIF2S3Y/ZFY-USP9Y-DBY/UTY)-(TSPY-SMCY-UBE1Y-SRY)-CEN. This gene order showed greater conservation with the murine Y than with the human Y Chr. In addition, all porcine Y Chr genes mapped to Yp, which is similar to the mouse and included EIF2s3Y and UBE1Y, which are not present in humans. Interestingly, complete conservation of X/Y homologous gene order was found between the pig X and Y Chrs, indicating that the porcine Y Chr has not undergone extensive reorganisation with respect to the X. This suggests that the order of the X/Y homologous genes of the porcine X and Y Chrs may closely resemble the ancestral gene order of the eutherian sex chromosomes.

Animals↗