Featured Research

from universities, journals, and other organizations

Comprehensive transcriptome analysis of human ENCODE cells

Date:
September 5, 2012
Source:
RIKEN
Summary:
ENCODE, an international research project led by the National Human Genome Research Institute (NHGRI), has produced and analyzed 1649 data sets designed to annotate functional elements of the entire human genome. Data on transcription starting sites (TSS) contributed by a research team at the RIKEN Omics Science Center provided key anchor points linking the epigenetic status of genes observed at the 5' end directly to their RNA output.

ENCODE, an international research project led by the National Human Genome Research Institute (NHGRI), has produced and analyzed 1649 data sets designed to annotate functional elements of the entire human genome. Data on transcription starting sites (TSS) contributed by a research team at the RIKEN Omics Science Center provided key anchor points linking the epigenetic status of genes observed at the 5' end directly to their RNA output.

The ENCODE (Encyclopedia of DNA Elements) project aims to delineate all functional elements encoded in the human genome. Thirty-two institutes from five countries have contributed to the project, each providing their own unique technologies and expertise. The project has developed methods and performed a large number of sequence-based studies mapping functional elements including RNA transcribed regions, protein-coding regions, transcription-factor-binding sites, chromatin structure, and DNA methylation sites.

A team of researchers at the RIKEN Omics Science Center led by Dr. Piero Carninci contributed to the mapping of RNA transcribed regions through their identification of TSSs using RIKEN's original CAGE technique. Subcellular compartments (whole cells, nuclei, and cytosol) from 15 cell lines were fractionated before RNA isolation. For one particular cell line (K562), further fractionation was performed to obtain chromatin, nucleoplasm, and nucleoli.

Isolated RNAs were then divided depending on their length, and long RNAs were further fractioned into polyadenylated and non-polyadenylated long RNA's. Each of the RNA fractions were then characterized for function analysis.

The data set was integrated with data sets provided by other research groups for further analysis, which included modeling transcription levels from histone modification/transcription factor-binding patterns and prediction of transcription activities at distal enhancer regions. Overall, this comprehensive data, together with other data sets, contributed to assigning biochemical functions for 80% of the human genome, particularly in areas outside of well-studied protein-coding regions. Another striking result is the pervasive presence of lowly-expressed RNA transcripts, whose localization is restricted to the cell nucleus.

"Scientists at the RIKEN Omics Science Center are particularly pleased with this work because the CAGE technology, developed earlier, was employed as one of the standard technologies for analyzing the output of the genome," Dr. Carninci said. "This international collaboration is in line with the OSC mission to understand the function of the genome. OSC has pioneered the field with the Fantom project, which provided a first comprehensive annotation of the mouse and human genome using CAGE, and identified a transcriptional network that controls the cell fate. The current ENCODE dataset provides a comprehensive set of data that strengthens and complements our previous and current work, aimed at understanding the function and regulation of the genome in health and disease states. OSC is committed to further characterize the genome output for much larger number of cells."


Story Source:

The above story is based on materials provided by RIKEN. Note: Materials may be edited for content and length.


Cite This Page:

RIKEN. "Comprehensive transcriptome analysis of human ENCODE cells." ScienceDaily. ScienceDaily, 5 September 2012. <www.sciencedaily.com/releases/2012/09/120905134916.htm>.
RIKEN. (2012, September 5). Comprehensive transcriptome analysis of human ENCODE cells. ScienceDaily. Retrieved July 23, 2014 from www.sciencedaily.com/releases/2012/09/120905134916.htm
RIKEN. "Comprehensive transcriptome analysis of human ENCODE cells." ScienceDaily. www.sciencedaily.com/releases/2012/09/120905134916.htm (accessed July 23, 2014).

Share This




More Health & Medicine News

Wednesday, July 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Courts Conflicted Over Healthcare Law

Courts Conflicted Over Healthcare Law

AP (July 22, 2014) Two federal appeals courts issued conflicting rulings Tuesday on the legality of the federally-run healthcare exchange that operates in 36 states. (July 22) Video provided by AP
Powered by NewsLook.com
Why Do People Believe We Only Use 10 Percent Of Our Brains?

Why Do People Believe We Only Use 10 Percent Of Our Brains?

Newsy (July 22, 2014) The new sci-fi thriller "Lucy" is making people question whether we really use all our brainpower. But, as scientists have insisted for years, we do. Video provided by Newsy
Powered by NewsLook.com
Scientists Find New Way To Make Human Platelets

Scientists Find New Way To Make Human Platelets

Newsy (July 22, 2014) Boston scientists have discovered a new way to create fully functioning human platelets using a bioreactor and human stem cells. Video provided by Newsy
Powered by NewsLook.com
Gilead's $1000-a-Pill Drug Could Cure Hep C in HIV-Positive People

Gilead's $1000-a-Pill Drug Could Cure Hep C in HIV-Positive People

TheStreet (July 21, 2014) New research shows Gilead Science's drug Sovaldi helps in curing hepatitis C in those who suffer from HIV. In a medical study, the combination of Gilead's Hep C drug with anti-viral drug Ribavirin cured 76% of HIV-positive patients suffering from the most common hepatitis C strain. Hepatitis C and related complications have been a top cause of death in HIV-positive patients. Typical medication used to treat the disease, including interferon proteins, tended to react badly with HIV drugs. However, Sovaldi's %1,000-a-pill price tag could limit the number of patients able to access the treatment. TheStreet's Keris Lahiff reports from New York. Video provided by TheStreet
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

More Coverage


Allegedly Useless Parts of the Human Genome Fulfil Regulatory Tasks

Sep. 7, 2012 Heidelberg scientists contribute to the encyclopedia of all functional DNA elements in the human ... read more
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins