Search Results for: mammalian genome transcript

Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells

lncRNA

The mammalian genome harbors thousands of long noncoding RNA (lncRNA) genes. Recent studies have indicated the involvement of several of these lncRNAs in the regulation of gene expression. lncRNAs play crucial roles in various biological processes ranging from epigenetic gene regulation, transcriptional control, to post-transcriptional regulation. lncRNAs are localized in various subcellular compartments, and major proportion of these are retained in the cell nucleus and could be broadly classified as nuclear-retained lncRNAs (nrRNAs). Based on the identified functions, members of the nrRNAs execute diverse roles, including providing architectural support to the hierarchical subnuclear organization and influencing the recruitment of chromatin modifier factors to specific chromatin sites. In this review, the authors summarize the recently described roles of mammalian nrRNAs in controlling gene expression by influencing chromatin organization, transcription, pre-mRNA processing, nuclear organization, and their involvement in disease.

  • Singh DK, Prasanth KV. (2013) Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells. Chromosome Res [Epub ahead of print]. [abstract]

Incoming search terms:

  • Evolutionary conservation of long non-coding RNAs; sequence structure function pdf
  • lncRNAs and nuclear compartments

Identification of novel transcripts and noncoding RNAs in bovine skin by RNA-Seq

lncRNA

Deep RNA sequencing (RNA-Seq) has opened a new horizon for understanding global gene expression. The functional annotation of non-model mammalian genomes including bovines is still poor compared to that of human and mouse. This particularly applies to tissues without direct significance for milk and meat production, like skin, in spite of its multifunctional relevance for the individual.

Here, researchers fromthe  Leibniz Institute for Farm Animal Biology, Germany performed a whole transcriptome analysis of pigmented and nonpigmented bovine skin to describe the comprehensive transcript catalogue of this tissue. A total of 39,577 unique primary skin transcripts were mapped to the bovine reference genome assembly. The majority of the transcripts were mapped to known transcriptional units (65%). In addition to the reannotation of known genes, a substantial number (10,884) of unknown transcripts (UTs) were discovered, which had not previously been annotated. The classification of UTs was based on the prediction of their coding potential and comparative sequence analysis, subsequently followed by meticulous manual curation. The classification analysis and experimental validation of selected UTs confirmed that RNA-Seq data can be used to amend the annotation of known genes by providing evidence for additional exons, untranslated regions or splice variants, by approving genes predicted in silico and by identifying novel bovine loci. A large group of UTs (4,848) was predicted to potentially represent long noncoding RNA (lncRNA). Predominantly, potential lncRNAs mapped in intergenic chromosome regions (4,365) and therefore, were classified as potential intergenic lncRNA. This analysis revealed that only about 6% of all UTs displayed interspecies conservation and discovered a variety of unknown transcripts without interspecies homology but specific expression in bovine skin.

The results of this study demonstrate a complex transcript pattern for bovine skin and suggest a possible functional relevance of novel transcripts, including lncRNA, in the modulation of pigmentation processes. The results also indicate that the comprehensive identification and annotation of unknown transcripts from whole transcriptome analysis using RNA-Seq data remains a tremendous future challenge.

  • Weikard R, Hadlich F, Kuehn C. (2013) Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing. BMC Genomics 14(1), 789. [abstract]

Incoming search terms:

  • ncrna rna-seq sense of transcription
  • rna sequencing bovine

The vast, conserved mammalian lincRNome

lncRNA

Genome analysis of humans and other mammals reveals a surprisingly small number of protein-coding genes, only slightly over 20,000 (although the diversity of actual proteins is substantially augmented by alternative transcription and alternative splicing). Recent analysis of the mammalian genomes and transcriptomes, in particular, using the RNA-seq technology, shows that, in addition to protein-coding genes, mammalian genomes encode many long non-coding RNAs. For some of these transcripts, various regulatory functions have been demonstrated, but on the whole the repertoire of long non-coding RNAs remains poorly characterized. Researchers at NCBI, NIH compared the identified long intergenic non-coding (linc)RNAs from human and mouse, and employed a specially developed statistical technique to estimate the size and evolutionary conservation of the human and mouse lincRNomes. The estimates show that there are at least twice as many human and mouse lincRNAs than there are protein-coding genes. Moreover, about two third of the lincRNA genes appear to be conserved between human and mouse, implying thousands of conserved but still uncharacterized functions.

Managadze D, Lobkovsky AE, Wolf YI, Shabalina SA, Rogozin IB, et al. (2013) The Vast, Conserved Mammalian lincRNome. PLoS Comput Biol 9(2), e1002917. [article]

Incoming search terms:

  • mammalian transcriptome
  • the vast conserved mammalian lincRNome

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

lncRNA

Mammalian genomes encode thousands of large noncoding RNAs (lncRNAs), many of which regulate gene expression, interact with chromatin regulatory complexes, and are thought to play a role in localizing these complexes to target loci across the genome. A paradigm for this class of lncRNAs is Xist, which orchestrates mammalian X-chromosome inactivation (XCI) by coating and silencing one X chromosome in females. Despite the central role of RNA-chromatin interactions in this process, the mechanisms by which Xist localizes to DNA and spreads across the X chromosome remain unknown.

Here, researchers at the Broad Institute of Harvard and MIT show that during the maintenance of XCI, Xist binds broadly across the X chromosome, lacking defined localization sites. Xist preferentially localizes to broad gene-dense regions and excludes genes that escape XCI. At the initiation of XCI in mouse embryonic stem cells, Xist initially transfers to distal regions across the X chromosome that are not defined by specific sequences. Instead, Xist RNA identifies these regions using a proximity-guided search mechanism, exploiting the three-dimensional conformation of the X chromosome to spread to distal regions in close spatial proximity to the Xist genomic locus. Initially, Xist is excluded from actively transcribed genes and accumulates on the periphery of regions containing many active genes. Xist requires its silencing domain to spread across these regions and access the entire chromosome.

The data presented in this study suggest a model for how Xist can integrate its two functions—localization to DNA and silencing of gene expression—to coat the entire X chromosome. In this model, Xist exploits three-dimensional conformation to identify and localize to initial target sites and leads to repositioning of these regions into the growing Xist compartment. These structural changes effectively pull new regions of the chromosome closer to the Xist genomic locus, allowing Xist RNA to spread to these newly accessible sites by proximity transfer. This localization strategy capitalizes on the abilities of a lncRNA to act while tethered to its transcription locus and to interact with chromatin regulatory proteins to modify chromatin structure. Beyond Xist, other lncRNAs may use a similar strategy to locate regulatory targets in three-dimensional proximity and to alter chromatin structure to establish local nuclear compartments containing co-regulated targets.

  • Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M. (2013) The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341(6147), 1237973. [abstract]

Incoming search terms:

  • lncRNA localization
  • lncrna mit
  • the xist lncrna exploits three- researcharticle dimensional genome architecture to spread across the x chromosome
  • xist lncrna genome location

Regulation of Mammalian Gene Dosage by Long Noncoding RNAs

lncRNA

Recent transcriptome studies suggest that long noncoding RNAs (lncRNAs) are key components of the mammalian genome, and their study has become a new frontier in biomedical research. In fact, lncRNAs in the mammalian genome were identified and studied at particular epigenetic loci, including imprinted loci and X-chromosome inactivation center, at least two decades ago—long before development of high throughput sequencing technology. Since then, researchers have found that lncRNAs play essential roles in various biological processes, mostly during development. Since much of our understanding of lncRNAs originates from our knowledge of these well-established lncRNAs, in this review the authors focus on lncRNAs from the X-chromosome inactivation center and the Dlk1-Dio3 imprinted cluster as examples of lncRNA mechanisms functioning in the epigenetic regulation of mammalian genes.

  • Hung KH, Wang Y, Zhao JC. (2013) Regulation of Mammalian Gene Dosage by Long Noncoding RNAs. Biomolecules 3(1), 124-142. [article]

Incoming search terms:

  • examples and nonexamples of genes