Literature DB >> 24653207

Examining the process of de novo gene birth: an educational primer on "integration of new genes into cellular networks, and their structural maturation".

Seth Frietze1, Judith Leatherman.   

Abstract

New genes that arise from modification of the noncoding portion of a genome rather than being duplicated from parent genes are called de novo genes. These genes, identified by their brief evolution and lack of parent genes, provide an opportunity to study the timeframe in which emerging genes integrate into cellular networks, and how the characteristics of these genes change as they mature into bona fide genes. An article by G. Abrusán provides an opportunity to introduce students to fundamental concepts in evolutionary and comparative genetics and to provide a technical background by which to discuss systems biology approaches when studying the evolutionary process of gene birth. Basic background needed to understand the Abrusán study and details on comparative genomic concepts tailored for a classroom discussion are provided, including discussion questions and a supplemental exercise on navigating a genome database.

Keywords:  cellular network; de novo genes; placeholder; secondary structure prediction; systems biology

Mesh:

Substances:

Year:  2014        PMID: 24653207      PMCID: PMC3948792          DOI: 10.1534/genetics.113.160895

Source DB:  PubMed          Journal:  Genetics        ISSN: 0016-6731            Impact factor:   4.562


  17 in total

1.  Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.

Authors:  Jill Cheng; Philipp Kapranov; Jorg Drenkow; Sujit Dike; Shane Brubaker; Sandeep Patel; Jeffrey Long; David Stern; Hari Tammana; Gregg Helt; Victor Sementchenko; Antonio Piccolboni; Stefan Bekiranov; Dione K Bailey; Madhavan Ganesh; Srinka Ghosh; Ian Bell; Daniela S Gerhard; Thomas R Gingeras
Journal:  Science       Date:  2005-03-24       Impact factor: 47.728

2.  TimeTree: a public knowledge-base of divergence times among organisms.

Authors:  S Blair Hedges; Joel Dudley; Sudhir Kumar
Journal:  Bioinformatics       Date:  2006-10-04       Impact factor: 6.937

Review 3.  What is a gene, post-ENCODE? History and updated definition.

Authors:  Mark B Gerstein; Can Bruce; Joel S Rozowsky; Deyou Zheng; Jiang Du; Jan O Korbel; Olof Emanuelsson; Zhengdong D Zhang; Sherman Weissman; Michael Snyder
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

Review 4.  The life and death of gene families.

Authors:  Jeffery P Demuth; Matthew W Hahn
Journal:  Bioessays       Date:  2009-01       Impact factor: 4.345

5.  Integration of new genes into cellular networks, and their structural maturation.

Authors:  György Abrusán
Journal:  Genetics       Date:  2013-09-20       Impact factor: 4.562

6.  Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast.

Authors:  Adam M Deutschbauer; Daniel F Jaramillo; Michael Proctor; Jochen Kumm; Maureen E Hillenmeyer; Ronald W Davis; Corey Nislow; Guri Giaever
Journal:  Genetics       Date:  2005-02-16       Impact factor: 4.562

7.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.

Authors:  E A Winzeler; D D Shoemaker; A Astromoff; H Liang; K Anderson; B Andre; R Bangham; R Benito; J D Boeke; H Bussey; A M Chu; C Connelly; K Davis; F Dietrich; S W Dow; M El Bakkoury; F Foury; S H Friend; E Gentalen; G Giaever; J H Hegemann; T Jones; M Laub; H Liao; N Liebundguth; D J Lockhart; A Lucau-Danila; M Lussier; N M'Rabet; P Menard; M Mittmann; C Pai; C Rebischung; J L Revuelta; L Riles; C J Roberts; P Ross-MacDonald; B Scherens; M Snyder; S Sookhai-Mahadeo; R K Storms; S Véronneau; M Voet; G Volckaert; T R Ward; R Wysocki; G S Yen; K Yu; K Zimmermann; P Philippsen; M Johnston; R W Davis
Journal:  Science       Date:  1999-08-06       Impact factor: 47.728

8.  The genetic landscape of a cell.

Authors:  Michael Costanzo; Anastasia Baryshnikova; Jeremy Bellay; Yungil Kim; Eric D Spear; Carolyn S Sevier; Huiming Ding; Judice L Y Koh; Kiana Toufighi; Sara Mostafavi; Jeany Prinz; Robert P St Onge; Benjamin VanderSluis; Taras Makhnevych; Franco J Vizeacoumar; Solmaz Alizadeh; Sondra Bahr; Renee L Brost; Yiqun Chen; Murat Cokol; Raamesh Deshpande; Zhijian Li; Zhen-Yuan Lin; Wendy Liang; Michaela Marback; Jadine Paw; Bryan-Joseph San Luis; Ermira Shuteriqi; Amy Hin Yan Tong; Nydia van Dyk; Iain M Wallace; Joseph A Whitney; Matthew T Weirauch; Guoqing Zhong; Hongwei Zhu; Walid A Houry; Michael Brudno; Sasan Ragibizadeh; Balázs Papp; Csaba Pál; Frederick P Roth; Guri Giaever; Corey Nislow; Olga G Troyanskaya; Howard Bussey; Gary D Bader; Anne-Claude Gingras; Quaid D Morris; Philip M Kim; Chris A Kaiser; Chad L Myers; Brenda J Andrews; Charles Boone
Journal:  Science       Date:  2010-01-22       Impact factor: 47.728

9.  YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.

Authors:  Dário Abdulrehman; Pedro Tiago Monteiro; Miguel Cacho Teixeira; Nuno Pereira Mira; Artur Bastos Lourenço; Sandra Costa dos Santos; Tânia Rodrigues Cabrito; Alexandre Paulo Francisco; Sara Cordeiro Madeira; Ricardo Santos Aires; Arlindo Limede Oliveira; Isabel Sá-Correia; Ana Teresa Freitas
Journal:  Nucleic Acids Res       Date:  2010-10-23       Impact factor: 16.971

10.  Novel genes exhibit distinct patterns of function acquisition and network integration.

Authors:  John A Capra; Katherine S Pollard; Mona Singh
Journal:  Genome Biol       Date:  2010-12-27       Impact factor: 13.583

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