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.

Related Articles


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 October 30, 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 October 30, 2014).

Share This



More Health & Medicine News

Thursday, October 30, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Mind-Controlled Prosthetic Arm Restores Amputee Dexterity

Mind-Controlled Prosthetic Arm Restores Amputee Dexterity

Reuters - Innovations Video Online (Oct. 29, 2014) A Swedish amputee who became the first person to ever receive a brain controlled prosthetic arm is able to manipulate and handle delicate objects with an unprecedented level of dexterity. The device is connected directly to his bone, nerves and muscles, giving him the ability to control it with his thoughts. Matthew Stock reports. Video provided by Reuters
Powered by NewsLook.com
Google To Use Nanoparticles, Wearables To Detect Disease

Google To Use Nanoparticles, Wearables To Detect Disease

Newsy (Oct. 29, 2014) Google X wants to improve modern medicine with nanoparticles and a wearable device. It's all an attempt to tackle disease detection and prevention. Video provided by Newsy
Powered by NewsLook.com
Can Drinking Milk Lead To Early Death?

Can Drinking Milk Lead To Early Death?

Newsy (Oct. 29, 2014) Researchers in Sweden released a study showing heavy milk drinkers face an increased mortality risk from a variety of causes. Video provided by Newsy
Powered by NewsLook.com
Obama: The US Will Not 'run and Hide' From Ebola

Obama: The US Will Not 'run and Hide' From Ebola

AP (Oct. 29, 2014) Surrounded by health care workers in the White House East Room, President Barack Obama said the U.S. will likely see additional Ebola cases in the weeks ahead. But he said the nation can't seal itself off in the fight against the disease. (Oct. 29) Video provided by AP
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

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

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