Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

BMC Genomics
Olgert DenasJames Taylor

Abstract

Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. Despite active experimental and computational research, relationships among sequence, conservation, and function are still poorly understood. We compared transcription factor occupied segments (TFos) for 116 human and 35 mouse TFs in 546 human and 125 mouse cell types and tissues from the Human and the Mouse ENCODE projects. We based the map between human and mouse TFos on a one-to-one nucleotide cross-species mapper, bnMapper, that utilizes whole genome alignments (WGA). Our analysis shows that TFos are under evolutionary constraint, but a substantial portion (25.1% of mouse and 25.85% of human on average) of the TFos does not have a homologous sequence on the other species; this portion varies among cell types and TFs. Furthermore, 47.67% and 57.01% of the homologous TFos sequence shows binding activity on the other species for human and mouse respectively. However, 79.87% and 69.22% is repurposed such that it binds the same TF in different cells or different TFs in the same cells. ...Continue Reading

References

Apr 11, 1975·Science·M C King, A C Wilson
Feb 17, 1968·Nature·M Kimura
Jul 25, 1969·Science·R J Britten, E H Davidson
Feb 3, 1999·Annual Review of Genetics·A L Hughes, M Yeager
Feb 28, 2001·Proceedings of the National Academy of Sciences of the United States of America·W J SwansonC F Aquadro
Aug 23, 2002·Nature·Wolfgang EnardSvante Pääbo
Jan 17, 2003·Genome Research·Scott SchwartzWebb Miller
Apr 3, 2003·Nature Reviews. Genetics·Abel Ureta-VidalEwan Birney
Sep 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·W James KentDavid Haussler
Oct 21, 2005·Nature·Carlos D BustamanteAndrew G Clark
Feb 14, 2006·Science·Eric H Davidson, Douglas H Erwin
May 25, 2006·Annual Review of Genomics and Human Genetics·Glenn A MastonMichael R Green
Feb 14, 2007·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Ryan J TaftJohn S Mattick
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Aug 11, 2007·Genome Research·Michael Pheasant, John S Mattick
Sep 13, 2008·Science·Michael D WilsonDuncan T Odom
Nov 17, 2009·Current Opinion in Genetics & Development·Michael D Wilson, Duncan T Odom
Jan 20, 2010·Trends in Genetics : TIG·Matthew T Weirauch, Timothy R Hughes
Aug 10, 2010·Genome Research·Stephen MeaderGerton Lunter
Aug 31, 2011·Genome Research·Chris P Ponting, Ross C Hardison
Nov 17, 2011·Nucleic Acids Research·Timothy R DreszerW James Kent
Jun 19, 2012·Nature Reviews. Genetics·Ross C Hardison, James Taylor
Aug 15, 2012·Genome Biology·UNKNOWN Mouse ENCODE ConsortiumLeslie B Adams
Sep 8, 2012·Nature·Robert E ThurmanJohn A Stamatoyannopoulos
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder
Dec 4, 2012·Nucleic Acids Research·Paul FlicekStephen M J Searle
Nov 21, 2014·Nature·Feng YueUNKNOWN Mouse ENCODE Consortium

❮ Previous
Next ❯

Citations

Dec 15, 2015·Ageing Research Reviews·Sukhleen Kour, Pramod C Rath
Jan 12, 2016·Molecular Neurobiology·Sukhleen Kour, Pramod C Rath
Sep 24, 2015·International Journal of Developmental Neuroscience : the Official Journal of the International Society for Developmental Neuroscience·Sukhleen Kour, Pramod C Rath
Sep 14, 2015·International Journal of Developmental Neuroscience : the Official Journal of the International Society for Developmental Neuroscience·Sukhleen Kour, Pramod C Rath
Jul 13, 2016·Human Molecular Genetics·Candice J CoppolaEric M Mendenhall
May 10, 2017·Nature Reviews. Genetics·Alessandra BreschiRoderic Guigó
May 18, 2017·Nature·Mary PhilipAndrea Schietinger
Jul 25, 2017·Nature Reviews. Genetics·Jennifer R S Meadows, Kerstin Lindblad-Toh
Mar 13, 2018·Briefings in Functional Genomics·Georgi K Marinov, Anshul Kundaje
Dec 6, 2017·Proceedings of the National Academy of Sciences of the United States of America·Julieta L MateosGeorge Coupland
Jul 31, 2018·Genome Biology and Evolution·Jouni KvistLeda Mirbahai
Feb 23, 2017·Frontiers in Endocrinology·Samantha Laber, Roger D Cox
Aug 15, 2018·Scientific Reports·Angela Di BaldassarreBarbara Ghinassi
Jan 4, 2020·The European Respiratory Journal·Mark Metersky, Grant Waterer
Mar 15, 2020·Science China. Life Sciences·Yingying ZengJing-Dong J Han
Sep 12, 2018·BMC Bioinformatics·Mario A Flores, Ivan Ovcharenko
Oct 8, 2020·Scientific Reports·Vasilis F NtasisChristoforos Nikolaou
Feb 28, 2021·Nature Communications·Ricardo D'Oliveira AlbanusStephen C J Parker

❮ Previous
Next ❯

Methods Mentioned

BETA
phylogenetic profiling
ChIP-Seq

Software Mentioned

blastz
UCSC browser
FunctActive
UCSC
Ensembl
bnMapper
FunctCons
EPO
SeqCons

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.