Literature DB >> 24995867

Genome-wide identification and characterization of fixed human-specific regulatory regions.

Davide Marnetto1, Ivan Molineris1, Elena Grassi1, Paolo Provero2.   

Abstract

Changes in gene regulatory networks are believed to have played an important role in the development of human-specific anatomy and behavior. We identified the human genome regions that show the typical chromatin marks of regulatory regions but cannot be aligned to other mammalian genomes. Most of these regions have become fixed in the human genome. Their regulatory targets are enriched in genes involved in neural processes, CNS development, and diseases such as autism, depression, and schizophrenia. Specific transposable elements contributing to the rewiring of the human regulatory network can be identified by the creation of human-specific regulatory regions. Our results confirm the relevance of regulatory evolution in the emergence of human traits and cognitive abilities and the importance of newly acquired genomic elements for such evolution.
Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

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Year:  2014        PMID: 24995867      PMCID: PMC4085640          DOI: 10.1016/j.ajhg.2014.05.011

Source DB:  PubMed          Journal:  Am J Hum Genet        ISSN: 0002-9297            Impact factor:   11.025


  43 in total

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Review 2.  Evolution at two levels in humans and chimpanzees.

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3.  Using GOstats to test gene lists for GO term association.

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4.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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5.  Convergent adaptation of human lactase persistence in Africa and Europe.

Authors:  Sarah A Tishkoff; Floyd A Reed; Alessia Ranciaro; Benjamin F Voight; Courtney C Babbitt; Jesse S Silverman; Kweli Powell; Holly M Mortensen; Jibril B Hirbo; Maha Osman; Muntaser Ibrahim; Sabah A Omar; Godfrey Lema; Thomas B Nyambo; Jilur Ghori; Suzannah Bumpstead; Jonathan K Pritchard; Gregory A Wray; Panos Deloukas
Journal:  Nat Genet       Date:  2006-12-10       Impact factor: 38.330

6.  The human enhancer blocker CTC-binding factor interacts with the transcription factor Kaiso.

Authors:  Pierre-Antoine Defossez; Kevin F Kelly; Guillaume J P Filion; Roberto Pérez-Torrado; Frédérique Magdinier; Hervé Menoni; Curtis L Nordgaard; Juliet M Daniel; Eric Gilson
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7.  Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence.

Authors:  Ian J Donaldson; Berthold Göttgens
Journal:  Genome Biol       Date:  2006       Impact factor: 13.583

Review 8.  Evolution at two levels: on genes and form.

Authors:  Sean B Carroll
Journal:  PLoS Biol       Date:  2005-07-12       Impact factor: 8.029

9.  Dynamics of DNA methylation in recent human and great ape evolution.

Authors:  Irene Hernando-Herraez; Javier Prado-Martinez; Paras Garg; Marcos Fernandez-Callejo; Holger Heyn; Christina Hvilsom; Arcadi Navarro; Manel Esteller; Andrew J Sharp; Tomas Marques-Bonet
Journal:  PLoS Genet       Date:  2013-09-05       Impact factor: 5.917

10.  The COUP-TF nuclear receptors regulate cell migration in the mammalian basal forebrain.

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  9 in total

1.  Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

Authors:  Gennadi V Glinsky
Journal:  Chromosome Res       Date:  2018-01-15       Impact factor: 5.239

2.  Evolutionary Rewiring of Human Regulatory Networks by Waves of Genome Expansion.

Authors:  Davide Marnetto; Federica Mantica; Ivan Molineris; Elena Grassi; Igor Pesando; Paolo Provero
Journal:  Am J Hum Genet       Date:  2018-01-18       Impact factor: 11.025

3.  Transposable elements are the primary source of novelty in primate gene regulation.

Authors:  Marco Trizzino; YoSon Park; Marcia Holsbach-Beltrame; Katherine Aracena; Katelyn Mika; Minal Caliskan; George H Perry; Vincent J Lynch; Christopher D Brown
Journal:  Genome Res       Date:  2017-08-30       Impact factor: 9.043

4.  Lung function associated gene Integrator Complex subunit 12 regulates protein synthesis pathways.

Authors:  Alexander K Kheirallah; Cornelia H de Moor; Alen Faiz; Ian Sayers; Ian P Hall
Journal:  BMC Genomics       Date:  2017-03-23       Impact factor: 3.969

5.  Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex.

Authors:  Guia Guffanti; Andrew Bartlett; Torsten Klengel; Claudia Klengel; Richard Hunter; Gennadi Glinsky; Fabio Macciardi
Journal:  Mol Biol Evol       Date:  2018-10-01       Impact factor: 16.240

6.  Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.

Authors:  David Gokhman; Rachel M Agoglia; Maia Kinnebrew; Wei Gordon; Danqiong Sun; Vivek K Bajpai; Sahin Naqvi; Coral Chen; Anthony Chan; Chider Chen; Dmitri A Petrov; Nadav Ahituv; Honghao Zhang; Yuji Mishina; Joanna Wysocka; Rajat Rohatgi; Hunter B Fraser
Journal:  Nat Genet       Date:  2021-03-17       Impact factor: 38.330

7.  Functional test of PCDHB11, the most human-specific neuronal surface protein.

Authors:  Guilherme Braga de Freitas; Rafaella Araújo Gonçalves; Matthias Gralle
Journal:  BMC Evol Biol       Date:  2016-04-12       Impact factor: 3.260

8.  Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

Authors:  Gennadi V Glinsky
Journal:  Genome Biol Evol       Date:  2016-09-19       Impact factor: 3.416

Review 9.  Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells.

Authors:  P Joel Ross; Rebecca S F Mok; Brandon S Smith; Deivid C Rodrigues; Marat Mufteev; Stephen W Scherer; James Ellis
Journal:  Mol Autism       Date:  2020-05-12       Impact factor: 7.509

  9 in total

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