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Functionality of Intergenic Transcription: An Evolutionary Comparison  [PDF]
Philipp Khaitovich equal contributor ,Janet Kelso equal contributor,Henriette Franz equal contributor,Johann Visagie,Thomas Giger,Sabrina Joerchel,Ekkehard Petzold,Richard E Green,Michael Lachmann,Svante P??bo
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020171
Abstract: Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts.
Inverted Repeats in Viral Genomes  [PDF]
M. Spano,F. Lillo,S. Micciche,R. N. Mantegna
Quantitative Biology , 2004,
Abstract: We investigate 738 complete genomes of viruses to detect the presence of short inverted repeats. The number of inverted repeats found is compared with the prediction obtained for a Bernoullian and for a Markovian control model. We find as a statistical regularity that the number of observed inverted repeats is often greater than the one expected in terms of a Bernoullian or Markovian model in several of the viruses and in almost all those with a genome longer than 30,000 bp.
MfSAT: Detect simple sequence repeats in viral genomes  [cached]
Ming Chen,Zhongyang Tan,Guangming Zeng
Bioinformation , 2011,
Abstract: Simple sequence repeats (SSRs) are ubiquitous short tandem repeats, which are associated with various regulatory mechanisms and have been found in viral genomes. Herein, we develop MfSAT (Multi-functional SSRs Analytical Tool), a new powerful tool which can fast identify SSRs in multiple short viral genomes and then automatically calculate the numbers and proportions of various SSR types (mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats). Furthermore, it also can detect codon repeats and report the corresponding amino acid.
Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs  [PDF]
Matthew J. Hangauer equal contributor,Ian W. Vaughn equal contributor,Michael T. McManus
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003569
Abstract: Known protein coding gene exons compose less than 3% of the human genome. The remaining 97% is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about the extent of intergenic transcription and whether these intergenic RNAs are functional. Here we directly observed with a large set of RNA-seq data covering a wide array of human tissue types that the majority of the genome is indeed transcribed, corroborating recent observations by the ENCODE project. Furthermore, using de novo transcriptome assembly of this RNA-seq data, we found that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known lincRNAs. In total, we identified tens of thousands of putative lincRNAs expressed at a minimum of one copy per cell, significantly expanding upon prior lincRNA annotation sets. These lincRNAs are specifically regulated and conserved rather than being the product of transcriptional noise. In addition, lincRNAs are strongly enriched for trait-associated SNPs suggesting a new mechanism by which intergenic trait-associated regions may function. These findings will enable the discovery and interrogation of novel intergenic functional elements.
Heterogeneity of Signal Transducer and Activator of Transcription Binding Sites in the Long-Terminal Repeats of Distinct HIV-1 Subtypes
Andrea Crotti, Giulia D. Chiara, Silvia Ghezzi, Rossella Lupo, Rienk E. Jeeninga, Elio Liboi, Patricia M.-J. Lievens, Elisa Vicenzi, Chiara Bovolenta, Ben BerkhoutGuido Poli
The Open Virology Journal , 2007, DOI: 10.2174/1874357900701010026]
Abstract: 26-32 Andrea Crotti, Giulia D. Chiara, Silvia Ghezzi, Rossella Lupo, Rienk E. Jeeninga, Elio Liboi, Patricia M.-J. Lievens, Elisa Vicenzi, Chiara Bovolenta, Ben Berkhout and Guido Poli Published Date: (28 September, 2007) HIV-1 can be subdivided into distinct subtypes; the consequences of such a genomic variability remain largely speculative. The long terminal repeats (LTR) control HIV transcription and reflect the major differences of distinct viral subtypes. Three regions in the HIV-1 subtype B LTR are close matches to the Signal Transducer and Activator of Transcription (STAT) consensus sequence. Here, we show heterogeneity in these putative STAT binding sites among HIV-1 LTR subtypes A through G. Transfection of constitutively activated STAT5 lead to transcriptional activation of HIV-1 expression in 293T cells transfected with a reporter assay driven by HIV-1 LTR subtype B. Constitutively activated STAT5 transactivated the LTR of various subtypes in U937 cells with different potency. These findings support and expand the potential relevance of STAT5 activation in HIV infection and may bear relevance for a differential regulation of latency and expression of different subtypes of HIV-1.
Intergenic Transcription, Cell-Cycle and the Developmentally Regulated Epigenetic Profile of the Human Beta-Globin Locus  [PDF]
Joanne Miles, Jennifer A. Mitchell, Lyubomira Chakalova, Beatriz Goyenechea, Cameron S. Osborne, Laura O'Neill, Keiji Tanimoto, James Douglas Engel, Peter Fraser
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000630
Abstract: Several lines of evidence have established strong links between transcriptional activity and specific post-translation modifications of histones. Here we show using RNA FISH that in erythroid cells, intergenic transcription in the human β-globin locus occurs over a region of greater than 250 kb including several genes in the nearby olfactory receptor gene cluster. This entire region is transcribed during S phase of the cell cycle. However, within this region there are ~20 kb sub-domains of high intergenic transcription that occurs outside of S phase. These sub-domains are developmentally regulated and enriched with high levels of active modifications primarily to histone H3. The sub-domains correspond to the β-globin locus control region, which is active at all developmental stages in erythroid cells, and the region flanking the developmentally regulated, active globin genes. These results correlate high levels of non-S phase intergenic transcription with domain-wide active histone modifications to histone H3.
Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq  [PDF]
Augix Guohua Xu ,Liu He ,Zhongshan Li ,Ying Xu,Mingfeng Li,Xing Fu,Zheng Yan,Yuan Yuan,Corinna Menzel,Na Li,Mehmet Somel,Hao Hu,Wei Chen ,Svante P??bo,Philipp Khaitovich
PLOS Computational Biology , 2010, DOI: 10.1371/journal.pcbi.1000843
Abstract: Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq) to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20–28% of non-ribosomal transcripts correspond to annotated exons and 20–23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40–48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20%) represents 3′UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits.
Epstein-Barr Nuclear Antigen 1 modulates replication of oriP-plasmids by impeding replication and transcription fork migration through the family of repeats
Ashok Aiyar, Siddhesh Aras, Amber Washington, Gyanendra Singh, Ronald B Luftig
Virology Journal , 2009, DOI: 10.1186/1743-422x-6-29
Abstract: We, and others, have determined previously that decreasing the number of EBNA1-binding sites in FR increases the efficiency with which oriP-plasmids are replicated. Here we demonstrate that the wild-type number of binding sites in FR impedes the migration of replication and transcription forks. Further, splitting FR into two widely separated sets of ten binding sites causes a ten-fold increase in the efficiency with which oriP-plasmids are established in cells expressing EBNA1. We have also determined that EBNA1 bound to FR impairs the migration of transcription forks in a manner dependent on the number of EBNA1-binding sites in FR.We conclude that EBNA1 bound to FR regulates the replication of oriP-plasmids by impeding the migration of replication forks. Upon binding FR, EBNA1 also blocks the migration of transcription forks. Thus, in addition to regulating oriP replication, EBNA1 bound to FR also decreases the probability of detrimental collisions between two opposing replication forks, or between a transcription fork and a replication fork.Epstein-Barr virus (EBV) is replicated once per cell-cycle as an episome in proliferating latently infected cells [1,2]. Episomal replication requires a viral sequence in cis, termed oriP, and a single viral protein EBNA1 [3,4]. OriP contains two sets of binding sites for EBNA1, the region of dyad symmetry (DS), that contains four sites of low affinity for EBNA1, and the family of repeats (FR) that contains twenty high-affinity sites for EBNA1 [5,6]. DNA synthesis initiates at DS, in a manner dependent upon the association of the cellular origin recognition complex (ORC) proteins and minichromosome maintenance (MCM) proteins with DS [7-9]. Recent evidence indicates that EBNA1 recruits the ORC proteins to DS through an RNA-mediated interaction with ORC1 [10].FR functions as a plasmid maintenance and partitioning element [11,12]. FR from the prototypic B95-8 strain of EBV contains 20 high-affinity sites for EBNA1, which binds eac
Trinucleotide repeats: triggers for genomic disorders?
Piotr Kozlowski, Krzysztof Sobczak, Wlodzimierz J Krzyzosiak
Genome Medicine , 2010, DOI: 10.1186/gm150
Abstract: At least a third of the human genome consists of repetitive sequences of various types, including large segmental duplications, also known as low-copy-number repeats (LCRs), long and short interspersed transposon-derived elements (LINEs and SINEs) and tandem repeats [1]. The tandemly repeated sequences encompass satellites (with repeated units longer than 100 bp), minisatellites (between 100 bp and 10 bp) and microsatellites (with a repeated motif shorter than 10 bp) [2]. The latter, also known as short tandem repeats (STRs) or simple sequence repeats, account for about 3% of the genome. Most of the STR tracts occur in the intergenic regions and introns, but a fraction of them, predominantly trinucleotide repeats (TNRs), also reside in exons and may be beneficial, neutral or deleterious. Among the beneficial roles of TNRs, which contribute about 0.1% to all STR sequences and are often polymorphic in length, is their potential to modulate cellular processes, including transcription splicing and translation [3]. These TNRs include repeats of CGG, CAG and AGG, which are overrepresented in human exons [4]. On the other hand, AAT, AAC and AAG are probably disadvantageous as they are negatively selected in exons [4]. TNR sequences undergo mutations at a very high frequency [5], and this may increase disease risk or trigger disease in specific conditions [6,7].Over the past two decades our thinking about the links between STRs and human diseases has been dominated by neurological disorders known as trinucleotide repeat expansion diseases (TREDs) [8,9]. There are over 20 diseases that belong to this group, the best known of which are fragile X syndrome (FXS), myotonic dystrophy type 1 (DM1), Huntington's disease (HD) and spinocerebellar ataxias (SCAs). FXS is caused by an expanded CGG repeat located in the 5' untranslated region (UTR) of the fragile X mental retardation 1 gene (FMR1); DM1 is triggered by an expanded CUG repeat located in the 3' UTR of the dystrophia myotoni
A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription
Tomas Babak, Benjamin J Blencowe, Timothy R Hughes
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-104
Abstract: To systematically search for functional ncRNAs, we designed microarrays to detect 3,478 intergenic and intronic sequences that are conserved between the human, mouse, and rat genomes, and that score highly by other criteria that characterize ncRNAs. We probed these arrays with total RNA isolated from 16 wild-type mouse tissues. Among 55 candidates for highly-expressed novel ncRNAs tested by northern blotting, eight were confirmed as small, highly-and ubiquitously-expressed RNAs in mouse. Of the eight, five were also detected in rat tissues, but none were detected at appreciable levels in human tissues or cultured cells.Since the sequence and expression of most known coding transcripts and functional ncRNAs is conserved between human and mouse, the lack of northern-detectable expression in human cells and tissues of the novel mouse and rat ncRNAs that we identified suggests that they are not functional or possibly have rodent-specific functions. Our results confirm that relatively little of the intergenic sequence conserved between human, mouse and rat is transcribed at high levels in mammalian tissues, possibly suggesting a limited role for transcribed intergenic and intronic sequences as independent functional elements.Comparative genomics has revealed that approximately 5% of the mammalian genome is under purifying selection [1,2]. While exons make up roughly 1.5% of the genome [3], relatively little is known about the role of the remaining 3.5% of the highly conserved genomic regions, and even less about the functional potential of evolutionarily-diverged intergenic sequences. Large-scale microarray tiling analyses (i.e. using a set of probes designed to detect all or most of a targeted genome or genomic region), as well as high-throughput cDNA sequencing efforts, have indicated that the "transcriptome" is significantly larger than was previously appreciated, although the functional significance of the vast majority of the novel, apparently noncoding (nc) transcr
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