Navigation Links
Modification of program enables prediction of gene transcription

A modification to an "ace" gene prediction program by computer scientists at Washington University in St. Louis now enables scientists to predict the very beginnings of gene transcription start sites and where the first splice occurs thereby defining the first exon of the gene.

The modification to the gene prediction software TWINSCAN is called N-SCAN. Michael Brent, Ph.D. professor of computer science at Washington University in St. Louis, together with Samuel S. Gross, then an undergraduate at Washington University, and Randall H. Brown, Ph.D., a research scientist, report their results in the May 2005 issue of Genome Research. N-SCAN has proven to be the best program available at finding both the transcription start site (TSS) and the complete first exon in both the human and fruit fly genomes.

The addition of N-SCAN to TWINSCAN now provides genomics researchers the wherewithal to find and predict both the protein sequences produced by genes and their untranslated regions. Researchers in recent years have grown increasingly enthusiastic about the significance of untranslated regions. By understanding the functions of these regions, scientists expect to understand more about gene regulation ?how genes get turned on and off, the ignition system of our DNA, if you will.

To make the proteins that are the basic micro-machines of life, a region of the genome is copied, or "transcribed," to form a molecule called messenger RNA (mRNA). Some segments of the mRNA are then discarded, and the retained segments are spliced together. Geneticists have traditionally assumed that transcription starts within a few hundred bases of the protein-coding region. However, for nearly 40 percent of known human genes, transcription starts long before the beginning of the protein- coding region. Most of this extra-long untranslated region is then discarded by splicing the 5' untranslated region (UTR). All present gene finding systems ?except for N-SCAN ?either ignore the UTR splice sites or incorrectly incorporate them into some protein-coding segment, making gene prediction a none-too-sure industry.

"We've found that when we add the spliced untranslated regions to our system, we not only get good predictions for UTRs but also improved predictions of the protein-coding region of the gene. By correctly identifying UTRs, we can avoid labeling them incorrectly as part of the protein-coding region," said Brent, who, with various colleagues, developed both TWINSCAN and N-SCAN. "It's important to know these two areas. Some of the signals that regulate transcription reside right near the transcription site. There is a huge amount of biology to be discovered there, and the appreciation of this area is growing daily."

While genomics researchers 15 years ago paid little attention to parts of the genome outside the coding regions, they have discovered some strange functions in UTR that have provoked second and third thoughts.

For instance, it recently was discovered that huntingtin, a gene associated with Huntington's disease, has a second protein segment encoded upstream of the main one. This protein in the so-called untranslated region is involved in regulating the gene. Running the modified TWINSCAN, on both the human and fruit fly genomes, Brent and colleagues predicted about 25,000 transcription-start sites, compared with a known 6,000.

"In the human genome, we found many extra exons on genes that were already known, or in some cases, spliced UTRs on genes that weren't even known to exist before," Brent said.

The system takes advantage of the scarcity of the CG sequence, finding so-called CpG "islands" known to be more common near the transcription-start site. It also has a knack for recognizing sequences that indicate splice sites. Over the past two years, TWINSCAN has been finding and predicting genes in numerous genomes that other gene prediction systems have missed. The addition of N-SCAN to the handy system ?it scans two genomes simultaneously, with potential to scan three or more ?strengthens it for predicting both coding and non-coding DNA.

"Like any multiple choice question, if you can learn something about one of the choices, it helps you with the other one," Brent said. "By making this integrated model that looks for both kinds of exons in both parts of the gene, we're able to convert a blind guessing game to a multiple choice question ?is it a UTR exon or a protein-coding exon? These kinds of questions are easier to answer now."


'"/>

Source:Washington University in St. Louis


Related biology news :

1. Modifications render carbon nanotubes nontoxic
2. Critical role in programmed cell death identified
3. Harmful chemicals may reprogram gene response to estrogen
4. Stem cell training program to make its Stanford debut
5. Rutgers to lead $52.7 million protein research program
6. DOEs Office of Science sets up program to aid scientists displaced by Hurricane Katrina
7. Costly breeding programs for endangered species pay off
8. HIV-infected adults in Botswana respond positively to ARV therapy public treatment program
9. Canine cancer vaccine program shows early promise
10. Its not fair! We are programmed to resist weight loss
11. Researchers unveil strategy for creating actively-programmed anti-cancer molecules
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:4/28/2016)... -- First quarter 2016:   , Revenues ... first quarter of 2015 The gross margin was 49% ... and the operating margin was 40% (-13) Earnings per ... from operations was SEK 249.9 M (21.2) , Outlook ... 7,000-8,500 M. The operating margin for 2016 is estimated ...
(Date:4/26/2016)... , April 27, 2016 ... "Global Multi-modal Biometrics Market 2016-2020"  report to their ... , The analysts forecast the global ... of 15.49% during the period 2016-2020.  ... of sectors such as the healthcare, BFSI, transportation, ...
(Date:4/15/2016)...  A new partnership announced today will help ... in a fraction of the time it takes ... life insurance policies to consumers without requiring inconvenient ... Diagnostics, rapid testing (A1C, Cotinine and HIV) and ... weight, pulse, BMI, and activity data) available at ...
Breaking Biology News(10 mins):
(Date:4/28/2016)... ... April 28, 2016 , ... Morris Midwest ( http://www.morrismidwest.com ), ... manufacturers at its Maple Grove, Minnesota technical center, May 11-12. The event ... Almost 20 leading suppliers of tooling, accessories, software and other related technology ...
(Date:4/27/2016)... York, NY (PRWEB) , ... April 27, 2016 ... ... realizing it. Touch screen mobile devices with fingerprint recognition for secure access, ... libraries are only a few ways consumers are interacting with biometrics technology today. ...
(Date:4/27/2016)... ... April 27, 2016 , ... NDA ... joined the company as an Expert Consultant. Mr. Clark was formerly a ... managing the development of small molecule monographs based on analytical methods. NDA ...
(Date:4/27/2016)... ... April 27, 2016 , ... Global Stem Cells Group ... Asia-Pacific Symposium as other research and development initiatives for potential stem cell protocol management ... Global Stem Cells Group executives began meeting to establish a working agenda and foster ...
Breaking Biology Technology: