Dynamic and widespread lncRNA expression in the sponge and the origin of animal complexity

Long non-coding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire More »

Featured lncRNA – PVT1

It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, More »

Researchers use RNA-Seq to show that lincRNAs can also contribute to HER2+ breast cancers

Ahmad M. Khalil, PhD, knew the odds were against him — as in thousands upon thousands to one. Yet he More »

Scientists develop a novel method to suppress malaria parasite’s virulence genes, break the code of its immune evasion

Revealed: how malaria evades the immune response by using long noncoding RNA to express one gene while silencing others Up More »

Long Noncoding RNAs in Cardiovascular Diseases

In recent years, increasing evidence suggests that noncoding RNAs play important roles in the regulation of tissue homeostasis and pathophysiological More »

 

GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development

Spermatogenic failure is a major cause of male infertility, which affects millions of couples worldwide. Recent discovery of long non-coding RNAs (lncRNAs) as critical regulators in normal and disease development provides new clues for delineating the molecular regulation in male germ cell development. However, few functional lncRNAs have been characterized to date. A major limitation in studying lncRNA in male germ cell development is the absence of germ cell-specific lncRNA annotation. Current lncRNA annotations are assembled by transcriptome data from heterogeneous tissue sources; specific germ cell transcript information of various developmental stages is therefore under-represented, which may lead to biased prediction or fail to identity important germ cell-specific lncRNAs.

GermlncRNA provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This information has been developed by integrating male germ transcriptome resources derived from RNA-Seq, tiling microarray and GermSAGE. Characterizations on lncRNA-associated regulatory features, potential coding gene and microRNA targets are also provided. Search results from GermlncRNA can be exported to Galaxy for downstream analysis or downloaded locally. Taken together, GermlncRNA offers a new avenue to better understand the role of lncRNAs and associated targets during spermatogenesis.

lncRNA

Availability – Database URL: http://germlncrna.cbiit.cuhk.edu.hk/

  • Luk AC, Gao H, Xiao S, Liao J, Wang D, Tu J, Rennert OM, Chan WY, Lee TL. (2015) GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development. Database (Oxford) bav044. [abstract]

Dynamic and widespread lncRNA expression in the sponge and the origin of animal complexity

lncRNA

Long non-coding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire expansion and morphological complexity in vertebrate evolution. However, this claim has not been tested by examining morphologically simple animals.

Here, researchers from the University of Queensland undertake a systematic investigation of lncRNAs in the demosponge Amphimedon queenslandica, a morphologically-simple, early-branching metazoan. They combine RNA-Seq data across multiple developmental stages of Amphimedon with a filtering pipeline to conservatively predict 2,935 lncRNAs. These include intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, long intergenic ncRNAs and precursors for small RNAs. Sponge lncRNAs are remarkably similar to their bilaterian counterparts in being relatively short with few exons and having low primary sequence conservation relative to protein-coding genes. As in bilaterians, a majority of sponge lncRNAs exhibit typical hallmarks of regulatory molecules, including high temporal specificity and dynamic developmental expression. Specific lncRNA expression profiles correlate tightly with conserved protein-coding genes likely involved in a range of developmental and physiological processes, such as the Wnt signaling pathway. Although the majority of Amphimedon lncRNAs appear to be taxonomically-restricted with no identifiable orthologues, the researchers find a few cases of conservation between demosponges in lncRNAs that are antisense to coding sequences. Based on the high similarity in the structure, organisation and dynamic expression of sponge lncRNAs to their bilaterian counterparts, they propose that these non-coding RNAs are an ancient feature of the metazoan genome. These results are consistent with lncRNAs regulating the development of animals, regardless of their level of morphological complexity.

  • Gaiti F, Fernandez-Valverde SL, Nakanishi N, Calcino AD, Yanai I, Tanurdzic M, Degnan BM. (2015) Dynamic and widespread lncRNA expression in the sponge and the origin of animal complexity. Mol Biol Evol [Epub ahead of print]. [abstract]

A Post-doctoral position is available – binding partners of non-annotated lncRNAs in vascular cells

lncRNAA Post-doctoral position is available immediately to study the binding partners of several non-annotated lncRNAs in vascular cells of human origin.

The position will require the candidate to have expertise in biochemical assays for the discovery of proteins or RNAs that interact with a number of nuclear and cytoplasmic

lncRNAs found through RNA-seq of human vascular cells treated under a variety of conditions.  The sponsor’s lab, located in brand new space within the University of Rochester Medical Center’s Cardiovascular Research Institute (see http://www.urmc.rochester.edu/cvri/ ), is well funded and has many projects related to lncRNAs and the emerging CRISPR-Cas9 genome editing system.  Applicants should be highly motivated with a goal of developing an independent research program for faculty-hood.  Applicants should submit their CV, 2 letters of reference and a brief synopsis of their research interests and skills to j.m.miano@rochester.edu

The University of Rochester is an equal opportunity employer.

Featured lncRNA – PVT1

lncRNA

It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, and (mis)function. However, while the functional characterization of short non-coding RNAs has been reaching maturity, there is still a paucity of well characterized long noncoding RNAs, even though large studies in recent years are rapidly increasing the number of annotated ones.

The long noncoding RNA PVT1 is encoded by a gene that has been long known since it resides in the well-known cancer risk region 8q24. However, a couple of accidental concurrent conditions have slowed down the study of this gene, that is, a preconception on the primacy of the protein-coding over noncoding RNAs and the prevalent interest in its neighbor MYC oncogene. Recent studies have brought PVT1 under the spotlight suggesting interesting models of functioning, such as competing endogenous RNA activity and regulation of protein stability of important oncogenes, primarily of the MYC oncogene. Despite some advancements in modelling the PVT1 role in cancer, there are many questions that remain unanswered concerning the precise molecular mechanisms underlying its functioning.

  • Colombo T, Farina L, Macino G, Paci P. (2015) PVT1: A Rising Star among Oncogenic Long Noncoding RNAs. Biomed Res Int 2015:304208. [article]

Postdoc position available – Johns Hopkins University

lncRNA

Highly motivated postdoctoral candidates are invited to lead several new projects to address fundamental questions in Biology. Current directions in the lab include nucleic acid interactions with proteins and small molecules, and microRNA biology.

The Johns Hopkins Medical Institutions provide a stimulating and collaborative environment for biomedical research. Our lab is affiliated with the Department of Biochemistry and Molecular Biology of the Bloomberg School of Public Health and the Department of Neuroscience of the School of Medicine. The Baltimore/Washington D.C. area also offers rich professional and living opportunities.

Candidates should have a doctoral degree and strong research background. Please send a statement of research experience and career goals, a copy of Curriculum Vitae, and contact information of at least one reference to Dr. Jiou Wang at jiouw@jhmi.edu.

More information available at: http://www.jhsph.edu/faculty/directory/profile/5049/Wang/Jiou. The Johns Hopkins University is an Equal Opportunity Employer.