Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems

Tal Shay; Vladimir Jojic; Or Zuk; Christophe Benoist; Daphne Koller; Aviv Regev; Paul Monach; Susan A. Shinton; Richard R. Hardy; Radu Jianu; David Laidlaw; Jim Collins; Roi Gazit; Brian S. Garrison; Derrick J. Rossi; Kavitha Narayan; Katelyn Sylvia; Joonsoo Kang; Anne Fletcher; Kutlu Elpek; Angelique Bel-lemare-Pelletier; Deepali Malhotra; Shannon Turley; Adam J. Best; Jamie Knell; Ananda Goldrath; Vladimir Jojic; Daphne Koller; Tal Shay; Aviv Regev; Nadia Cohen; Patrick Brennan; Michael Brenner; Taras Kreslavsky; Natalie A. Bezman; Joseph C. Sun; Charlie C. Kim; Lewis L. Lanier; Jennifer Miller; Brian Brown; Miriam Merad; Emmanuel L. Gautier; Claudia Jakubzick; Gwendalyn J. Randolph; Francis Kim; Tata Nageswara Rao; Amy Wagers; Tracy Heng; Michio Painter; Jeffrey Ericson; Scott Davis; Ayla Ergun; Michael Mingueneau; Diane Mathis; Christophe Benoist

doi:10.1101/286211

Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems

Tal Shay, Vladimir Jojic, Or Zuk, Christophe Benoist, Daphne Koller, Aviv Regev, Paul Monach, Susan A. Shinton, Richard R. Hardy, Radu Jianu, David Laidlaw, Jim Collins, Roi Gazit, Brian S. Garrison, Derrick J. Rossi, Kavitha Narayan, Katelyn Sylvia, Joonsoo Kang, Anne Fletcher, Kutlu ElpekAngelique Bel-lemare-Pelletier, Deepali Malhotra, Shannon Turley, Adam J. Best, Jamie Knell, Ananda Goldrath, Vladimir Jojic, Daphne Koller, Tal Shay, Aviv Regev, Nadia Cohen, Patrick Brennan, Michael Brenner, Taras Kreslavsky, Natalie A. Bezman, Joseph C. Sun, Charlie C. Kim, Lewis L. Lanier, Jennifer Miller, Brian Brown, Miriam Merad, Emmanuel L. Gautier, Claudia Jakubzick, Gwendalyn J. Randolph, Francis Kim, Tata Nageswara Rao, Amy Wagers, Tracy Heng, Michio Painter, Jeffrey Ericson, Scott Davis, Ayla Ergun, Michael Mingueneau, Diane Mathis, Christophe Benoist

Department of Life Sciences

Research output: Working paper/Preprint › Preprint

Abstract

Studies in mouse models have played an important role in shedding light on human hematopoietic differentiation and disease. However, substantial differences between the two species often limit the translation of findings from mouse to human. Here, we complement our previous comparative transcriptomics analysis of the human and mouse immune systems by assessing the conservation of co-expression of genes. By comparing previously defined modules of co-expressed genes in human and mouse immune cells based on compendia of genome-wide profiles, we show that the overall modular organization of the transcriptional program is indeed conserved across the two species. However, several modules of co-expressed genes in one species dissolve or split in the other species, indicating loss of co-expression. Many of the associated regulatory mechanisms – as reflected by computationally inferred trans-regulators or enriched cis-regulatory elements – are conserved across the two species. Nevertheless, the degree of conservation of regulatory mechanisms is lower than that of expression, suggesting that distinct regulation may underlie some conserved transcriptional responses.

Original language	English
Publisher	bioRxiv
DOIs	https://doi.org/10.1101/286211
State	Published - 22 Mar 2018

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Shay, T., Jojic, V., Zuk, O., Benoist, C., Koller, D., Regev, A., Monach, P., Shinton, S. A., Hardy, R. R., Jianu, R., Laidlaw, D., Collins, J., Gazit, R., Garrison, B. S., Rossi, D. J., Narayan, K., Sylvia, K., Kang, J., Fletcher, A., ... Benoist, C. (2018). Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems. (bioRxiv). bioRxiv. https://doi.org/10.1101/286211

@techreport{c6e76f0ac6ee4529a11d6494076e4edd,

title = "Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems",

abstract = "Studies in mouse models have played an important role in shedding light on human hematopoietic differentiation and disease. However, substantial differences between the two species often limit the translation of findings from mouse to human. Here, we complement our previous comparative transcriptomics analysis of the human and mouse immune systems by assessing the conservation of co-expression of genes. By comparing previously defined modules of co-expressed genes in human and mouse immune cells based on compendia of genome-wide profiles, we show that the overall modular organization of the transcriptional program is indeed conserved across the two species. However, several modules of co-expressed genes in one species dissolve or split in the other species, indicating loss of co-expression. Many of the associated regulatory mechanisms – as reflected by computationally inferred trans-regulators or enriched cis-regulatory elements – are conserved across the two species. Nevertheless, the degree of conservation of regulatory mechanisms is lower than that of expression, suggesting that distinct regulation may underlie some conserved transcriptional responses.",

author = "Tal Shay and Vladimir Jojic and Or Zuk and Christophe Benoist and Daphne Koller and Aviv Regev and Paul Monach and Shinton, {Susan A.} and Hardy, {Richard R.} and Radu Jianu and David Laidlaw and Jim Collins and Roi Gazit and Garrison, {Brian S.} and Rossi, {Derrick J.} and Kavitha Narayan and Katelyn Sylvia and Joonsoo Kang and Anne Fletcher and Kutlu Elpek and Angelique Bel-lemare-Pelletier and Deepali Malhotra and Shannon Turley and Best, {Adam J.} and Jamie Knell and Ananda Goldrath and Vladimir Jojic and Daphne Koller and Tal Shay and Aviv Regev and Nadia Cohen and Patrick Brennan and Michael Brenner and Taras Kreslavsky and Bezman, {Natalie A.} and Sun, {Joseph C.} and Kim, {Charlie C.} and Lanier, {Lewis L.} and Jennifer Miller and Brian Brown and Miriam Merad and Gautier, {Emmanuel L.} and Claudia Jakubzick and Randolph, {Gwendalyn J.} and Francis Kim and Rao, {Tata Nageswara} and Amy Wagers and Tracy Heng and Michio Painter and Jeffrey Ericson and Scott Davis and Ayla Ergun and Michael Mingueneau and Diane Mathis and Christophe Benoist",

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doi = "10.1101/286211",

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Shay, T, Jojic, V, Zuk, O, Benoist, C, Koller, D, Regev, A, Monach, P, Shinton, SA, Hardy, RR, Jianu, R, Laidlaw, D, Collins, J, Gazit, R, Garrison, BS, Rossi, DJ, Narayan, K, Sylvia, K, Kang, J, Fletcher, A, Elpek, K, Bel-lemare-Pelletier, A, Malhotra, D, Turley, S, Best, AJ, Knell, J, Goldrath, A, Jojic, V, Koller, D, Shay, T, Regev, A, Cohen, N, Brennan, P, Brenner, M, Kreslavsky, T, Bezman, NA, Sun, JC, Kim, CC, Lanier, LL, Miller, J, Brown, B, Merad, M, Gautier, EL, Jakubzick, C, Randolph, GJ, Kim, F, Rao, TN, Wagers, A, Heng, T, Painter, M, Ericson, J, Davis, S, Ergun, A, Mingueneau, M, Mathis, D & Benoist, C 2018 'Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems' bioRxiv, bioRxiv. https://doi.org/10.1101/286211

TY - UNPB

T1 - Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems

AU - Shay, Tal

AU - Jojic, Vladimir

AU - Zuk, Or

AU - Benoist, Christophe

AU - Koller, Daphne

AU - Regev, Aviv

AU - Monach, Paul

AU - Shinton, Susan A.

AU - Hardy, Richard R.

AU - Jianu, Radu

AU - Laidlaw, David

AU - Collins, Jim

AU - Gazit, Roi

AU - Garrison, Brian S.

AU - Rossi, Derrick J.

AU - Narayan, Kavitha

AU - Sylvia, Katelyn

AU - Kang, Joonsoo

AU - Fletcher, Anne

AU - Elpek, Kutlu

AU - Bel-lemare-Pelletier, Angelique

AU - Malhotra, Deepali

AU - Turley, Shannon

AU - Best, Adam J.

AU - Knell, Jamie

AU - Goldrath, Ananda

AU - Jojic, Vladimir

AU - Koller, Daphne

AU - Shay, Tal

AU - Regev, Aviv

AU - Cohen, Nadia

AU - Brennan, Patrick

AU - Brenner, Michael

AU - Kreslavsky, Taras

AU - Bezman, Natalie A.

AU - Sun, Joseph C.

AU - Kim, Charlie C.

AU - Lanier, Lewis L.

AU - Miller, Jennifer

AU - Brown, Brian

AU - Merad, Miriam

AU - Gautier, Emmanuel L.

AU - Jakubzick, Claudia

AU - Randolph, Gwendalyn J.

AU - Kim, Francis

AU - Rao, Tata Nageswara

AU - Wagers, Amy

AU - Heng, Tracy

AU - Painter, Michio

AU - Ericson, Jeffrey

AU - Davis, Scott

AU - Ergun, Ayla

AU - Mingueneau, Michael

AU - Mathis, Diane

AU - Benoist, Christophe

PY - 2018/3/22

Y1 - 2018/3/22

N2 - Studies in mouse models have played an important role in shedding light on human hematopoietic differentiation and disease. However, substantial differences between the two species often limit the translation of findings from mouse to human. Here, we complement our previous comparative transcriptomics analysis of the human and mouse immune systems by assessing the conservation of co-expression of genes. By comparing previously defined modules of co-expressed genes in human and mouse immune cells based on compendia of genome-wide profiles, we show that the overall modular organization of the transcriptional program is indeed conserved across the two species. However, several modules of co-expressed genes in one species dissolve or split in the other species, indicating loss of co-expression. Many of the associated regulatory mechanisms – as reflected by computationally inferred trans-regulators or enriched cis-regulatory elements – are conserved across the two species. Nevertheless, the degree of conservation of regulatory mechanisms is lower than that of expression, suggesting that distinct regulation may underlie some conserved transcriptional responses.

AB - Studies in mouse models have played an important role in shedding light on human hematopoietic differentiation and disease. However, substantial differences between the two species often limit the translation of findings from mouse to human. Here, we complement our previous comparative transcriptomics analysis of the human and mouse immune systems by assessing the conservation of co-expression of genes. By comparing previously defined modules of co-expressed genes in human and mouse immune cells based on compendia of genome-wide profiles, we show that the overall modular organization of the transcriptional program is indeed conserved across the two species. However, several modules of co-expressed genes in one species dissolve or split in the other species, indicating loss of co-expression. Many of the associated regulatory mechanisms – as reflected by computationally inferred trans-regulators or enriched cis-regulatory elements – are conserved across the two species. Nevertheless, the degree of conservation of regulatory mechanisms is lower than that of expression, suggesting that distinct regulation may underlie some conserved transcriptional responses.

UR - https://www.mendeley.com/catalogue/a81a0152-2c42-31bf-b93d-af142080d8a3/

U2 - 10.1101/286211

DO - 10.1101/286211

M3 - Preprint

T3 - bioRxiv

BT - Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems

PB - bioRxiv

ER -

Conservation and divergence in modules of the transcriptional programs of human and mouse immune systems

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