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Zhang, Haibo; Lee, Ju Youn; Tian, Bin

doi:10.1186/gb-2005-6-12-r100

Cited by 265 publications

(169 citation statements)

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“…Alternative mRNA splicing (21) and polyadenylation (3,4) significantly increase diversity of gene expression in male germ cells. CstF-64 is a candidate for controlling polyadenylation in male germ cells (8).…”

Section: Discussionmentioning

confidence: 99%

“…Although polyadenylation is nearly universal, features of polyadenylation are different in mammalian male germ cells than in other tissues: male germ cell mRNAs exhibit increased alternative polyadenylation (3,4), decreased use of the AAUAAA polyadenylation signal (5,6), and reduced dependence on downstream sequence elements (DSEs) (7). These differences suggest a modified mechanism for polyadenylation in male germ cells.…”

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confidence: 93%

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Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility

Dass

Tardif

Park

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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131

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Polyadenylation, the process of eukaryotic mRNA 3 end formation, is essential for gene expression and cell viability. Polyadenylation of male germ cell mRNAs is unusual, exhibiting increased alternative polyadenylation, decreased AAUAAA polyadenylation signal use, and reduced downstream sequence element dependence. CstF-64, the RNA-binding component of the cleavage stimulation factor (CstF), interacts with pre-mRNAs at sequences downstream of the cleavage site. In mammalian testes, meiotic XY-body formation causes suppression of X-linked CstF-64 expression during pachynema. Consequently, an autosomal paralog, CstF-64 (gene name Cstf2t), is expressed during meiosis and subsequent haploid differentiation. Here we show that targeted disruption of Cstf2t in mice causes aberrant spermatogenesis, specifically disrupting meiotic and postmeiotic development, resulting in male infertility resembling oligoasthenoteratozoospermia. Furthermore, the Cstf2t mutant phenotype displays variable expressivity such that spermatozoa show a broad range of defects. The overall phenotype is consistent with a requirement for CstF-64 in spermatogenesis as indicated by the significant changes in expression of thousands of genes in testes of Cstf2t ؊/؊ mice as measured by microarray. Our results indicate that, although the infertility in Cstf2t ؊/؊ males is due to low sperm count, multiple genes controlling many aspects of germ-cell development depend on CstF-64 for their normal expression. Finally, these transgenic mice provide a model for the study of polyadenylation in an isolated in vivo system and highlight the role of a growing family of testis-expressed autosomal retroposed variants of X-linked genes.spermatogenesis ͉ oligoasthenoteratozoospemia ͉ meiosis ͉ XY body ͉ meiotic sex chromosome inactivation P olyadenylation, the process of mRNA 3Ј end formation, is required for the synthesis, transport, translation, and stability of eukaryotic mRNAs (1, 2). Although polyadenylation is nearly universal, features of polyadenylation are different in mammalian male germ cells than in other tissues: male germ cell mRNAs exhibit increased alternative polyadenylation (3, 4), decreased use of the AAUAAA polyadenylation signal (5, 6), and reduced dependence on downstream sequence elements (DSEs) (7). These differences suggest a modified mechanism for polyadenylation in male germ cells.While examining these differences, we discovered CstF-64 (8), which is a paralog of the 64,000 M r subunit of the cleavage stimulation factor (CstF-64) (9-11). CstF-64 is expressed in nuclei of early spermatogenic cells (5, 12). However, because it is on the X chromosome, CstF-64 expression halts in pachytene spermatocytes because of meiotic sex chromosome inactivation (MSCI) (13). In contrast, CstF-64 expression begins in pachytene spermatocytes and continues in spermatocytes and early spermatids (refs. 5 and 12; summarized in Fig. 1). CstF-64 is the only known CstF-64 homolog expressed during male meiosis, thus making it a candidate to play a critical role in sper...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 93%

Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility

Dass

Tardif

Park

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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131

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“…However, the recent study of Derti and colleagues 27 alone resulted in a list of 280,000 human CP sites compared with 150,000 sites that were known from previous work. The advantage of these deep sequencing-based methods is that they enable us to move away from a binary (present/absent), ESTbased description, 28 or a semi-quantitative, microarray-based measurement 29 of polyadenylation site usage in specific libraries or tissues, toward precise quantification of alternative polyadenylation site use. This in turn allows exploration of the processing mechanism in various conditions and for different classes of transcripts such as the still poorly understood noncoding RNAs.…”

Section: Cleavagefactor I M Is a Key Regulator Of 3' Utr Lengthmentioning

confidence: 99%

Cleavage factor I_mis a key regulator of 3′ UTR length

Gruber

Martín²,

Keller³

et al. 2012

RNA Biology

129

122

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“…To further study the usage of alternative poly(A) sites in each library, we used a method similar to GAUGE (Zhang et al 2005), with small modifications. In each library, the expression values of each signature (TPM value) were grouped based on their APA classes.…”

Section: Library-specific Data Analysismentioning

confidence: 99%

“…Previous EST-based analyses showed that about a half of human and rice genes and up to one-third of algal protein-coding genes undergo APA (Zhang et al 2005;Shen et al 2008a,b), suggesting that APA has a global role in the regulation of gene expression. The cost and efficiency of EST-based data for APA studies, however, limit the number of poly(A) sites that can be found and prevent the study of APA in greater depth.…”

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confidence: 99%

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

Shen

Venu²,

Nobuta³

et al. 2011

Genome Res.

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Polyadenylation sites mark the ends of mRNA transcripts. Alternative polyadenylation (APA) may alter sequence elements and/or the coding capacity of transcripts, a mechanism that has been demonstrated to regulate gene expression and transcriptome diversity. To study the role of APA in transcriptome dynamics, we analyzed a large-scale data set of RNA “tags” that signify poly(A) sites and expression levels of mRNA. These tags were derived from a wide range of tissues and developmental stages that were mutated or exposed to environmental treatments, and generated using digital gene expression (DGE)–based protocols of the massively parallel signature sequencing (MPSS-DGE) and the Illumina sequencing-by-synthesis (SBS-DGE) sequencing platforms. The data offer a global view of APA and how it contributes to transcriptome dynamics. Upon analysis of these data, we found that ∼60% of Arabidopsis genes have multiple poly(A) sites. Likewise, ∼47% and 82% of rice genes use APA, supported by MPSS-DGE and SBS-DGE tags, respectively. In both species, ∼49%–66% of APA events were mapped upstream of annotated stop codons. Interestingly, 10% of the transcriptomes are made up of APA transcripts that are differentially distributed among developmental stages and in tissues responding to environmental stresses, providing an additional level of transcriptome dynamics. Examples of pollen-specific APA switching and salicylic acid treatment-specific APA clearly demonstrated such dynamics. The significance of these APAs is more evident in the 3034 genes that have conserved APA events between rice and Arabidopsis.

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Cited by 265 publications

References 52 publications

Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility

Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility

Cleavage factor I_mis a key regulator of 3′ UTR length

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

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Untitled

Cited by 265 publications

References 52 publications

Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility

Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility

Cleavage factor Imis a key regulator of 3′ UTR length

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

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Cleavage factor I_mis a key regulator of 3′ UTR length