Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs

The role of noncoding RNAs in mammalian biology is of great interest, especially since the Encyclopedia of DNA Elements results More »

The Long Noncoding RNA Expression Profile of Hepatocellular Carcinoma Identified by Microarray Analysis

Thousands of long noncoding RNAs (lncRNAs) have been reported in mammalian genomes. These RNAs represent an important subset of pervasive More »

lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). More »

Long non-coding RNAs: evolution of new epigenetic and post-transcriptional functions

9:00 am on Monday 28 September 2015 — 5:00 pm on Tuesday 29 September 2015 at The Royal Society at More »

Featured long non-coding RNA – meiRNA

Long non-coding RNAs (lncRNAs) play key roles in the formation of nuclear bodies. In the fission yeast Schizosaccharomyces pombe, a More »

 

LncRNA: A link between RNA and cancer

Unraveling the gene expression networks governing cancer initiation and development is essential while remains largely uncompleted. With the innovations in RNA-seq technologies and computational biology, long noncoding RNAs (lncRNAs) are being identified and characterized at a rapid pace. Recent findings reveal that lncRNAs are implicated in serial steps of cancer development. These lncRNAs interact with DNA, RNA, protein molecules and/or their combinations, acting as an essential regulator in chromatin organization, transcriptional and post-transcriptional regulation. Their misexpression confers the cancer cell capacities for tumor initiation, growth, and metastasis. The review here will emphasize their aberrant expression and function in cancer, and the roles in cancer diagnosis and therapy will be also discussed.

lncRNA

  • Yanga G, Lub X, Yuanc L. (2014) LncRNA: A link between RNA and cancer. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms [Epub ahead of print]. [abstract]

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs

Notch signaling is a key developmental pathway that is subject to frequent genetic and epigenetic perturbations in many different human tumors.

Here a team led by researchers from the NYU School of Medicine investigate whether long noncoding RNA (lncRNA) genes, in addition to mRNAs, are key downstream targets of oncogenic Notch1 in human T cell acute lymphoblastic leukemia (T-ALL). By integrating transcriptome profiles with chromatin state maps, they have uncovered many previously unreported T-ALL-specific lncRNA genes, a fraction of which are directly controlled by the Notch1/Rpbjκ activator complex. Finally they have shown that one specific Notch-regulated lncRNA, LUNAR1, is required for efficient T-ALL growth in vitro and in vivo due to its ability to enhance IGF1R mRNA expression and sustain IGF1 signaling. These results confirm that lncRNAs are important downstream targets of the Notch signaling pathway, and additionally they are key regulators of the oncogenic state in T-ALL.

lncRNA

  • Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, Aifantis I. (2014) Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia. Cell 158(3):593-606. [abstract]

Postdoc Position Available – Myc regulated lncRNAs in B-cell lymphoma

 

Department Department of Pathology & Medical Biology
Work location Groningen
Apply no later than 14 September 2014

lncRNAWorking environment

Project description
Our lab is interested in understanding the function of non-coding RNAs in B-cell lymphoma. Besides studying microRNAs for over ten years, we more recently gained interest in the function of long non-coding RNAs in B cell lymphoma. Long non-coding RNAs are an exciting group of transcripts involved in many cell physiological processes, and deregulation of them has been associated with many diseases such as cancer. One of the important oncogenes in B-cell lymphoma is the transcription factor Myc that is known to regulate expression of a large number of genes that are important for malignant transformation. Using a comprehensive gene expression analysis approach, we recently identified a group of Myc-regulated long non-coding RNAs. The objective of this project funded by the pediatric oncology foundation Groningen (SKOG) is to determine to what extend these long non-coding RNAs are involved in the pathogenesis of Myc-associated B-cell lymphoma and to unveil the underlying mechanisms.

Our Research group is located at the Department of Pathology & Medical Biology and we have close collaborations with the Departments of Genetics and Hematology. The research line is embedded within the Cancer Research Center Groningen. The focus of this research center is to initiate and stimulate the translation of fundamental insights from preclinical research programs on oncogenesis and tumor behavior into cancer prevention, improvement of early detection of cancer and better treatment for cancer patients. The non-coding B cell lymphoma group is part of the Stem cells Aging, Leukemia and Lymphoma (SALL) subprogram which includes various research groups of the Hematology, Stem cell biology, Pediatric oncology and Pathology. Besides an excellent international scientific environment we have state-of-the-art research facilities including those needed for NGS, imaging, qRT-PCR, array analysis and many others.

What do we need

  • PhD in molecular biology, cancer research or equivalent.
  • You are an outstanding enthusiastic scientist who is pro-active, independent and motivated to setup assays to mechanistically study lncRNAs.
  • You are a team player and aim to pursue a career in scientific research.
  • You have experience with diverse molecular biology techniques and bioinformatics analysis is a strong advantage.
  • You have excellent English skills, both oral and written.
  • Experience in writing scientific papers and presentation of your work at scientific meetings.
  • Experience in supervision of students and technicians.
  • Fascination for non-coding RNA is an advantage.

The UMCG has a preventive Hepatitis B policy. You may be required to build up sufficient protection against Hepatitis B before you can be appointed. Vaccination is provided by the UMCG if necessary.

What do we offer

  • A postdoc position according to conditions of employment that comply with the Collective Labor Agreement for Medical Centers (CAO-UMC).
  • A contract for one year with a second year extension after positive evaluation.
  • Based on qualifications and experience a maximum salary of € 4.070,- gross a month (scale 10) for a fulltime position.

More information
For more information about this vacancy you may contact:
Mr. Dr. J. Kluiver, molecular biologist, phone: +31 50 3615788, email: j.l.kluiver@umcg.nl (please do not use for applications).
Ms. Prof. dr. A. van den Berg, molecular biologist, phone: +31 50 3611476, email: a.van.den.berg01@umcg.nl (please do not use for applications).

Applying for a job

Please use the the digital application form at the bottom of this page – only these will be processed.
You can apply until 14 September 2014.
Immediately after sending the digital application form you will receive an email- confirmation with further information.
(Learn more…)

Apply

A long non-coding RNA signature to improve prognosis prediction of colorectal cancer

Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis.

Researchers from the Shanghai Institution of Digestive Disease aimed to develop a lncRNA signature to improve prognosis prediction of colorectal cancer (CRC). Using a lncRNA-mining approach, they performed lncRNA expression profiling in large CRC cohorts from Gene Expression Ominus (GEO) (N=436), internal validation series (N=117); and two independent validation series GSE14333 (N=197) and GSE17536(N=145). They established a set of six lncRNAs that were significantly correlated with the disease free survival (DFS) in the test series. Based on this six-lncRNA signature, the test series patients could be classified into high-risk and low-risk subgroups with significantly different DFS (HR=2.670; P<0.0001). The prognostic value of this six-lncRNA signature was confirmed in the internal validation series and another two independent CRC sets. Gene set enrichment analysis (GSEA) analysis suggested that risk score positively correlated with several cancer metastasis related pathways. Functional experiments demonstrated three dysregulated lncRNAs, AK123657, BX648207 and BX649059 were required for efficient invasion and proliferation suppression in CRC cell lines. Our results might provide an efficient classification tool for clinical prognosis evaluation of CRC.

lncRNA

  • Hu Y1, Chen HY, Yu CY, Xu J, Wang JL, Qian J, Zhang X, Fang JY. (2014) A long non-coding RNA signature to improve prognosis prediction of colorectal cancer. Oncotarget 5(8):2230-42. [article]

Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs

lncRNA

The role of noncoding RNAs in mammalian biology is of great interest, especially since the Encyclopedia of DNA Elements results were published. Many have studied microRNAs in the heart, but little is known about their larger cousins, long noncoding RNAs (lncRNAs). Here, researchers from the Washington University School of Medicine used genome-wide sequencing and improved bioinformatics to quantify lncRNA expression in mouse hearts, define a subset of cardiac-specific lncRNAs, and measure dynamic lncRNA regulation during the transition between embryo and adult, and in the adult heart after experimental pressure overload (a model resembling human hypertensive cardiomyopathy). They linked specific regulated lncRNAs to cardiac-expressed mRNAs that they target and, through network analyses, discovered a broader role of regulated cardiac lncRNAs as modulators of key cardiac transcriptional pathways.

  • Matkovich SJ, Edwards JR, Grossenheider TC, de Guzman Strong C, Dorn GW 2nd. (2014) Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs. Proc Natl Acad Sci U S A 111(33):12264-9. [abstract]