Corporate Banner
Satellite Banner
Scientific Community
Become a Member | Sign in
Home>News>This Article

Scientists Looking Across Human, Fly and Worm Genomes Find Shared Biology

Published: Thursday, August 28, 2014
Last Updated: Thursday, August 28, 2014
Bookmark and Share
Studies reveal powerful commonalities in biological activity and regulation among species.

Researchers analyzing human, fly, and worm genomes have found that these species have a number of key genomic processes in common, reflecting their shared ancestry. The findings, appearing Aug. 28, 2014, in the journal Nature, offer insights into embryonic development, gene regulation and other biological processes vital to understanding human biology and disease.

The studies highlight the data generated by the modENCODE Project and the ENCODE Project, both supported by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health. Integrating data from the three species, the model organism ENCyclopedia Of DNA Elements (modENCODE) Consortium studied how gene expression patterns and regulatory proteins that help determine cell fate often share common features. Investigators also detailed the similar ways in which the three species use protein packaging to compact DNA into the cell nucleus and to regulate genome function by controlling access to DNA.

Launched in 2007, the goal of modENCODE is to create a comprehensive catalog of functional elements in the fruit fly and roundworm genomes for use by the research community. Such elements include genes that code for proteins, non-protein-coding genes and regulatory elements that control gene expression. The current work builds on initial catalogs published in 2010. The modENCODE projects complement the work being done by the ENCyclopedia Of DNA Elements (ENCODE) Project, which is building a comprehensive catalog of functional elements in the human and mouse genomes.

“The modENCODE investigators have provided a valuable resource for researchers worldwide,” said NHGRI Director Eric Green, M.D., Ph.D. “The insights gained about the workings of model organisms’ genomes greatly help to inform our understanding of human biology.”

“One way to describe and understand the human genome is through comparative genomics and studying model organisms,” said Mark Gerstein, Ph.D., Albert L. Williams Professor of Biomedical Informatics at Yale University in New Haven, Connecticut, and the lead author on one of the papers. “The special thing about the worm and fly is that they are very distant from humans evolutionarily, so finding something conserved across all three — human, fly and worm — tells us it is a very ancient, fundamental process.”

In one study, scientists led by Dr. Gerstein and others, analyzed human, fly and worm transcriptomes, the collection of gene transcripts (or readouts) in a genome. They used large amounts of gene expression data generated in the ENCODE and modENCODE projects — including more than 67 billion gene sequence readouts — to discover gene expression patterns shared by all three species, particularly for developmental genes.

Investigators showed that the ways in which DNA is packaged in the cell are similar in many respects, and, in many cases, the species share programs for turning on and off genes in a coordinated manner. More specifically, they used gene expression patterns to match the stages of worm and fly development and found sets of genes that parallel each other in their usage. They also found the genes specifically expressed in the worm and fly embryos are re-expressed in the fly pupae, the stage between larva and adult.

The researchers found that in all three organisms, the gene expression levels for both protein-coding and non-protein-coding genes could be quantitatively predicted from chromatin features at the promoters of genes. A gene’s promoter tells the cell’s machinery where to begin copying DNA into RNA, which can be used to make proteins. DNA is packaged into chromatin in cells, and changes in this packaging can regulate gene function.

“Our findings open whole new worlds for understanding gene expression and how we think about the role of transcription,” said co-senior author Susan Celniker, Ph.D., Head, Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California. “modENCODE has been transformative,” she added. “It has helped set the standard for the types of data that should be generated and catalogued.”

Another group of scientists investigated how chromatin is organized and how it influences gene regulation in the three species. Using both modENCODE and ENCODE data, scientists compared patterns of modifications in chromatin that are needed for the cell to access the DNA inside, and the changes in DNA replication patterns as a result of these modifications. The investigators discovered that many features of chromatin were similar in all three species.

“We found mostly that the usage of chromatin modification by the three organisms is highly conserved,” said co-senior author Jason Lieb, Ph.D., professor of human genetics, University of Chicago. He noted there is a great deal of interest in chromatin because of its potential connection to some diseases, such as cancer. A number of studies have shown that some cancers may be driven in part by mutations in chromatin-related genes.

In a third study, scientists explored similarities in genome regulation. Scientists focused on transcription-regulatory factors, key protein regulators that determine which progenitor cells eventually become skin cells and kidney cells and eye cells. “These are the key coordinators – they bind to switches that control a cell’s fate. One of the big questions in genomics is to determine what factors work together to turn on which genes,” said co-senior author Michael Snyder, Ph.D., director, Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, California.

Investigators found that the transcription factors tend to bind to similar DNA sequences in the three species’ genomes, indicating that “the general properties of how regulatory information is laid out in the genomes are conserved in the three species,” Dr. Snyder noted. “The general principles of regulation are more or less similar.” Still, they found differences as well. The transcription factors bind very few of the same targets across species, and they are mostly expressed at different times.

Including these newly published studies, more than a dozen modENCODE Consortium papers have been or will be published in the journals Nature, Genome Research, Genome Biology, and the Proceedings of the National Academy of Sciences this year. These additional papers report studies involving deeper analyses within one or more species, methods development and investigations of particular biological processes. This collection of papers is the culmination of the modENCODE program, for which funding ended in 2012. More than 100 papers using modENCODE data by groups outside of the program have already been published. It is anticipated that the data and resources produced by modENCODE will continue to be used by the broader research community for years to come.

Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,700+ scientific posters on ePosters
  • More than 3,800+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

NIH Breast Cancer Research to Focus On Prevention
A new phase of the Breast Cancer and the Environment Research Program (BCERP), focused on prevention, is being launched at the National Institutes of Health.
Friday, October 09, 2015
NIH Grantees Win 2015 Nobel Prize in Chemistry
The 2015 Nobel Prize in chemistry has been awarded to NIH grantees Paul Modrich, Ph.D., of the Howard Hughes Medical Institute and the Duke University School of Medicine, Durham, N.C.; and Aziz Sancar, M.D., Ph.D., of the University of North Carolina, Chapel Hill, N.C.,.
Thursday, October 08, 2015
New Gene Therapy for Vision Loss From a Mitochondrial Disease
NIH-funded study shows success in targeting mitochondrial DNA in mice.
Tuesday, October 06, 2015
NIH Funding Targets Gaps in Biomedical Research
New awards support emerging issues in cutting-edge biomedical research fields.
Tuesday, October 06, 2015
Scientists Test New Gene Therapy for Vision Loss from a Mitochondrial Disease
NIH-funded study shows success in targeting mitochondrial DNA in mice.
Tuesday, October 06, 2015
Dormant Viral Genes May Awaken to Cause ALS
NIH human and mouse study may open an unexplored path for finding treatments.
Thursday, October 01, 2015
Scientists Create World’s Largest Catalog of Human Genomic Variation
An international team of scientists from the 1000 Genomes Project Consortium has created the world’s largest catalog of genomic differences among humans, providing researchers with powerful clues to help them establish why some people are susceptible to various diseases.
Thursday, October 01, 2015
Genetic Adaptations to Diet and Climate
Researchers found genetic variations in the Inuit of Greenland that reflect adaptations to their specific diet and climate.
Tuesday, September 29, 2015
Grants to Help Identify Variants in the Genome’s Regulatory Regions
New computational approaches needed to wade through millions of inherited DNA differences to find which ones matter.
Thursday, September 24, 2015
Grants Awarded to Explore the Genome’s Regulatory Regions that Affect Disease Risk
New computational approaches needed to wade through millions of inherited DNA differences to find which ones matter.
Tuesday, September 22, 2015
NIH Framework Points The Way Forward For Developing The President’s Precision Medicine Initiative
The NIH Advisory Committee to the Director has presented to NIH Director Francis S. Collins, M.D., Ph.D., a detailed design framework for building a national research participant group, called a cohort, of 1 million or more Americans to expand our knowledge and practice of precision medicine.
Monday, September 21, 2015
Diet, Exercise, Smoking Habits and Genes Interact To Affect and Risk
NIH-funded study points to converging factors that drive disease-related inflammation.
Thursday, September 17, 2015
NIH Grants Seek Best Ways To Combine Genomic Information and EHRs
Researchers seek to better understand genomic basis of disease, provide tailored care to patients.
Friday, September 04, 2015
Cellular Factors that Shape the 3D Landscape of the Genome Identified
Researchers have identified 50 cellular factors required for the proper 3D positioning of genes by using novel large-scale imaging technology.
Tuesday, August 18, 2015
Nuclear Process in the Brain That May Affect Disease Uncovered
Scientists have shown that the passage of molecules through the nucleus of a star-shaped brain cell, called an astrocyte, may play a critical role in health and disease.
Tuesday, August 18, 2015
Scientific News
Gene Editing Could Enable Pig-To-Human Organ Transplant
The largest number of simultaneous gene edits ever accomplished in the genome could help bridge the gap between organ transplant scarcity and the countless patients who need them.
Antioxidants Cause Malignant Melanoma to Metastasize Faster
Fresh research at Sahlgrenska Academy has found that antioxidants can double the rate of melanoma metastasis in mice.
UC San Diego Team Up with Illumina to Speed-Read Your Microbiome
Data analysis app accelerates studies aimed at using microbes to predict, diagnose and treat human diseases.
Paving the Way for Diamonds to Trace Early Cancers
Researchers from the University of Sydney reveal how nanoscale 'diamonds' can light up early-stage cancers in MRI scans.
Researchers Develop Classification Model for Cancers Caused by KRAS
Most frequently mutated cancer gene help oncologists choose more effective cancer therapies.
Chromosomal Chaos
Penn study forms basis for future precision medicine approaches for Sezary syndrome
Shaking Up the Foundations of Epigenetics
Researchers at the Centre for Genomic Regulation (CRG) and the University of Barcelona (UB) published a study that challenges some of the current beliefs about epigenetics.
Genetic Defences of Bacteria Don’t Aid Antibiotic Resistance
Genetic responses to the stresses caused by antibiotics don’t help bacteria to evolve a resistance to the medications, according to a new study by Oxford University researchers.
Tolerant Immune System Increases Cancer Risk
Researchers have found that individuals with high immunoCRIT ratios may have an increased risk of developing certain cancers.
Developing a Gel that Mimics Human Breast for Cancer Research
Scientists at the Universities of Manchester and Nottingham have been funded to develop a gel that will match many of the biological structures of human breast tissue, to advance cancer research and reduce animal testing.
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,700+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,800+ scientific videos