Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Autor: John K. Mich, Lucas T. Graybuck, Erik E. Hess, Joseph T. Mahoney, Yoshiko Kojima, Yi Ding, Saroja Somasundaram, Jeremy A. Miller, Brian E. Kalmbach, Cristina Radaelli, Bryan B. Gore, Natalie Weed, Victoria Omstead, Yemeserach Bishaw, Nadiya V. Shapovalova, Refugio A. Martinez, Olivia Fong, Shenqin Yao, Marty Mortrud, Peter Chong, Luke Loftus, Darren Bertagnolli, Jeff Goldy, Tamara Casper, Nick Dee, Ximena Opitz-Araya, Ali Cetin, Kimberly A. Smith, Ryder P. Gwinn, Charles Cobbs, Andrew L. Ko, Jeffrey G. Ojemann, C. Dirk Keene, Daniel L. Silbergeld, Susan M. Sunkin, Viviana Gradinaru, Gregory D. Horwitz, Hongkui Zeng, Bosiljka Tasic, Ed S. Lein, Jonathan T. Ting, Boaz P. Levi

Publikováno v: Cell Reports, Vol 34, Iss 13, Pp 108754- (2021)

Summary: Viral genetic tools that target specific brain cell types could transform basic neuroscience and targeted gene therapy. Here, we use comparative open chromatin analysis to identify thousands of human-neocortical-subclass-specific putative en

Externí odkaz: https://doaj.org/article/f3fbdff3e4964a89bce059657aed05d2

Human neocortical expansion involves glutamatergic neuron diversification

Autor: Tim S. Heistek, Thomas Braun, Natalia A. Goriounova, Michael Tieu, Lindsay Ng, Michael Hawrylycz, Kris Bickley, Anton Arkhipov, Colin Farrell, Trangthanh Pham, Alexandra Glandon, Daniel Park, Gábor Molnár, Herman Tung, Allan R. Jones, Lisa Keene, Gáspár Oláh, Thomas Chartrand, Amy Torkelson, Jae Geun Yoon, Rachel A. Dalley, Aaron Szafer, Nick Dee, Brian E. Kalmbach, Eliza Barkan, Allison Beller, Krissy Brouner, Andrew L. Ko, Alex M. Henry, Viktor Szemenyei, Julie Nyhus, Staci A. Sorensen, Samuel Dingman Lee, Norbert Mihut, Amy Bernard, Lisa Kim, Anatoly Buchin, Melissa Gorham, Lucas T. Graybuck, Lydia Potekhina, Katelyn Ward, Caitlin S. Latimer, Aaron Oldre, Gabe J. Murphy, Boaz P. Levi, Trygve E. Bakken, René Wilbers, Jonathan T. Ting, Kimberly A. Smith, Amanda Gary, Songlin Ding, Alice Mukora, Matthew Kroll, Anoop P. Patel, Wayne Wakeman, Hongkui Zeng, Nadezhda Dotson, Rusty Mann, Victoria Omstead, Leona Mezei, Desiree A. Marshall, Shea Ransford, Lydia Ng, Sara Kebede, Gábor Tamás, Jeffrey G. Ojemann, Stephanie Mok, Nathan Hansen, Christina A. Pom, Brian Lee, Jim Berg, Ramkumar Rajanbabu, John W. Phillips, Philip R. Nicovich, Matthew Mallory, Richard G. Ellenbogen, Rachel Enstrom, Luke Esposito, Tim Jarsky, Di Jon Hill, Idan Segev, Darren Bertagnolli, Agata Budzillo, Sander Idema, Daniel L. Silbergeld, Costas A. Anastassiou, Chris Hill, Michelle Maxwell, Mean Hwan Kim, Charles Cobbs, Delissa McMillen, Bosiljka Tasic, Olivia Fong, Medea McGraw, Hong Gu, Kirsten Crichton, David Reid, Kristen Hadley, Lauren Alfiler, Manuel Ferreira, Elliot R. Thomsen, Kiet Ngo, Josef Sulc, Augustin Ruiz, Katherine Baker, Zizhen Yao, Erica J. Melief, Femke Waleboer, Hanchuan Peng, Grace Williams, Rebecca D. Hodge, Kyla Berry, Katherine E. Link, David Sandman, Tsega Desta, Christine Rimorin, Jeff Goldy, Ryder P. Gwinn, Djai B. Heyer, Changkyu Lee, Jeremy A. Miller, Nathan W. Gouwens, Pál Barzó, Attila Ozsvár, Huibert D. Mansvelder, Sergey L. Gratiy, Rafael Yuste, David Feng, Jessica Trinh, Clare Gamlin, Tamara Casper, C. Dirk Keene, Susan M. Sunkin, Tom Egdorf, Philip C. De Witt Hamer, Rebecca de Frates, Peter Chong, Szabina Furdan, Patrick R. Hof, Jasmine Bomben, Christiaan P. J. de Kock, Eline J. Mertens, Ed S. Lein, Anna A. Galakhova, Florence D’Orazi, Christof Koch, Madie Hupp

Publikováno v: Berg, J, Sorensen, S A, Ting, J T, Miller, J A, Chartrand, T, Buchin, A, Bakken, T E, Budzillo, A, Dee, N, Ding, S L, Gouwens, N W, Hodge, R D, Kalmbach, B, Lee, C, Lee, B R, Alfiler, L, Baker, K, Barkan, E, Beller, A, Berry, K, Bertagnolli, D, Bickley, K, Bomben, J, Braun, T, Brouner, K, Casper, T, Chong, P, Crichton, K, Dalley, R, de Frates, R, Desta, T, Lee, S D, D’Orazi, F, Dotson, N, Egdorf, T, Enstrom, R, Farrell, C, Feng, D, Fong, O, Furdan, S, Galakhova, A A, Gamlin, C, Gary, A, Glandon, A, Goldy, J, Gorham, M, Goriounova, N A, Gratiy, S, Graybuck, L, Gu, H, Hadley, K, Hansen, N, Heistek, T S, Henry, A M, Heyer, D B, Hill, D J, Hill, C, Hupp, M, Jarsky, T, Kebede, S, Keene, L, Kim, L, Kim, M H, Kroll, M, Latimer, C, Levi, B P, Link, K E, Mallory, M, Mann, R, Marshall, D, Maxwell, M, McGraw, M, McMillen, D, Melief, E, Mertens, E J, Mezei, L, Mihut, N, Mok, S, Molnar, G, Mukora, A, Ng, L, Ngo, K, Nicovich, P R, Nyhus, J, Olah, G, Oldre, A, Omstead, V, Ozsvar, A, Park, D, Peng, H, Pham, T, Pom, C A, Potekhina, L, Rajanbabu, R, Ransford, S, Reid, D, Rimorin, C, Ruiz, A, Sandman, D, Sulc, J, Sunkin, S M, Szafer, A, Szemenyei, V, Thomsen, E R, Tieu, M, Torkelson, A, Trinh, J, Tung, H, Wakeman, W, Waleboer, F, Ward, K, Wilbers, R, Williams, G, Yao, Z, Yoon, J G, Anastassiou, C, Arkhipov, A, Barzo, P, Bernard, A, Cobbs, C, de Witt Hamer, P C, Ellenbogen, R G, Esposito, L, Ferreira, M, Gwinn, R P, Hawrylycz, M J, Hof, P R, Idema, S, Jones, A R, Keene, C D, Ko, A L, Murphy, G J, Ng, L, Ojemann, J G, Patel, A P, Phillips, J W, Silbergeld, D L, Smith, K, Tasic, B, Yuste, R, Segev, I, de Kock, C P J, Mansvelder, H D, Tamas, G, Zeng, H, Koch, C & Lein, E S 2021, ' Human neocortical expansion involves glutamatergic neuron diversification ', Nature, vol. 598, no. 7879, pp. 151-158 . https://doi.org/10.1038/s41586-021-03813-8
Nature, 598(7879), 151-158. Nature Publishing Group
Nature
Nature, Vol. 598, No. 7879
Berg, J, Sorensen, S A, Ting, J T, Miller, J A, Chartrand, T, Buchin, A, Bakken, T E, Budzillo, A, Dee, N, Ding, S-L, Gouwens, N W, Hodge, R D, Kalmbach, B, Lee, C, Lee, B R, Alfiler, L, Baker, K, Barkan, E, Beller, A, Berry, K, Bertagnolli, D, Bickley, K, Bomben, J, Braun, T, Brouner, K, Casper, T, Chong, P, Crichton, K, Dalley, R, de Frates, R, Desta, T, Lee, S D, D’Orazi, F, Dotson, N, Egdorf, T, Enstrom, R, Farrell, C, Feng, D, Fong, O, Furdan, S, Galakhova, A A, Gamlin, C, Gary, A, Glandon, A, Goldy, J, Gorham, M, Goriounova, N A, Gratiy, S, Graybuck, L, Gu, H, Hadley, K, Hansen, N, Heistek, T S, Henry, A M, Heyer, D B, Hill, D, Hill, C, Hupp, M, Jarsky, T, Kebede, S, Keene, L, Kim, L, Kim, M-H, Kroll, M, Latimer, C, Levi, B P, Link, K E, Mallory, M, Mann, R, Marshall, D, Maxwell, M, McGraw, M, McMillen, D, Melief, E, Mertens, E J, Mezei, L, Mihut, N, Mok, S, Molnar, G, Mukora, A, Ng, L, Ngo, K, Nicovich, P R, Nyhus, J, Olah, G, Oldre, A, Omstead, V, Ozsvar, A, Park, D, Peng, H, Pham, T, Pom, C A, Potekhina, L, Rajanbabu, R, Ransford, S, Reid, D, Rimorin, C, Ruiz, A, Sandman, D, Sulc, J, Sunkin, S M, Szafer, A, Szemenyei, V, Thomsen, E R, Tieu, M, Torkelson, A, Trinh, J, Tung, H, Wakeman, W, Waleboer, F, Ward, K, Wilbers, R, Williams, G, Yao, Z, Yoon, J-G, Anastassiou, C, Arkhipov, A, Barzo, P, Bernard, A, Cobbs, C, de Witt Hamer, P C, Ellenbogen, R G, Esposito, L, Ferreira, M, Gwinn, R P, Hawrylycz, M J, Hof, P R, Idema, S, Jones, A R, Keene, C D, Ko, A L, Murphy, G J, Ng, L, Ojemann, J G, Patel, A P, Phillips, J W, Silbergeld, D L, Smith, K, Tasic, B, Yuste, R, Segev, I, de Kock, C P J, Mansvelder, H D, Tamas, G, Zeng, H, Koch, C & Lein, E S 2021, ' Human neocortical expansion involves glutamatergic neuron diversification ', Nature, vol. 598, no. 7879, pp. 151-158 . https://doi.org/10.1038/s41586-021-03813-8

The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections wit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8c41f5015a297892f279cb761e2d9f21
https://hdl.handle.net/1871.1/df908a46-b182-41b3-b732-326dddbab23b

Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Autor: Joseph T. Mahoney, Kimberly A. Smith, Refugio A. Martinez, Victoria Omstead, Ed S. Lein, Natalie Weed, Lucas T. Graybuck, Darren Bertagnolli, Luke Loftus, Jeffrey G. Ojemann, Boaz P. Levi, Jonathan T. Ting, John K. Mich, Yoshiko Kojima, Gregory D. Horwitz, Tamara Casper, Jeff Goldy, Andrew L. Ko, Yi Ding, Bryan B. Gore, Cristina Radaelli, C. Dirk Keene, Olivia Fong, Viviana Gradinaru, Marty Mortrud, Ximena Opitz-Araya, Yemeserach Bishaw, Nick Dee, Nadiya V. Shapovalova, Brian E. Kalmbach, Jeremy A. Miller, Hongkui Zeng, Charles Cobbs, Bosiljka Tasic, Daniel L. Silbergeld, Shenqin Yao, Ali Cetin, Ryder P. Gwinn, Hess Erik, Saroja Somasundaram, Peter Chong, Susan M. Sunkin

Publikováno v: Cell Reports, Vol 34, Iss 13, Pp 108754-(2021)
Cell reports

SUMMARY Viral genetic tools that target specific brain cell types could transform basic neuroscience and targeted gene therapy. Here, we use comparative open chromatin analysis to identify thousands of human-neocortical-sub-class-specific putative en

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::837142427b14bce46b297cb2811b6e81
https://resolver.caltech.edu/CaltechAUTHORS:20200421-093728277

Regional, layer, and cell-class specific connectivity of the mouse default mode network

Autor: Ali Williford, Nile Graddis, Karla E. Hirokawa, Wayne Wakeman, Stefan Mihalas, Philip R. Nicovich, Thuc Nghi Nguyen, Olivia Fong, Adam Liska, Phillip Bohn, Anh Ho, Lydia Ng, Emma Garren, Boaz P. Levi, Kimberly A. Smith, Nick Dee, Julie A. Harris, David Feng, Alex M. Henry, Cindy T. J. van Velthoven, Peter A. Groblewski, Alessandro Gozzi, Jennifer D. Whitesell, Hongkui Zeng, Bosiljka Tasic, Maitham Naeemi, Joseph E. Knox, Leonard Kuan, Ludovico Coletta

The evolutionarily conserved default mode network (DMN) is characterized by temporally correlated activity between brain regions during resting states. The DMN has emerged as a selectively vulnerable network in multiple disorders, so understanding it

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3ef8ae652bbd36e91f244f34af0f5927

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Autor: Susan M. Sunkin, Qingzhong Ren, Michael Tieu, Fahimeh Baftizadeh, Kimberly A. Smith, Boaz P. Levi, Kanan Lathia, Olivia Fong, James Gray, Lucas T. Graybuck, Jeff Goldy, Bosiljka Tasic, Christine Rimorin, Thuc Nghi Nguyen, Kirsten Crichton, Josef Sulc, Songlin Ding, Darren Bertagnolli, Zizhen Yao, Hongkui Zeng, Delissa McMillen, Cindy T. J. van Velthoven, Katelyn Ward, Alexandra Glandon, Thanh Pham, Herman Tung, Amy Torkelson, Nick Dee, Nadiya V. Shapovalova, Stephanie Mok, Emma Garren, Matthew Kroll, Tamara Casper, Adriana E. Sedeno-Cortes, Daniel Hirschstein

SUMMARYThe isocortex and hippocampal formation are two major structures in the mammalian brain that play critical roles in perception, cognition, emotion and learning. Both structures contain multiple regions, for many of which the cellular compositi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::653919e9a1531a38cf23c9a9c7ff9701
https://doi.org/10.1101/2020.03.30.015214