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Disturbed mitochondrial dynamics in CD8+ TILs reinforce T cell exhaustion

Yu, Yi-Ru ; Imrichova, Hana ; Wang, Haiping ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Nature Immunology Vol. 21, No. 12 ( 2020-12), p. 1540-1551

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In: Nature Immunology, Springer Science and Business Media LLC, Vol. 21, No. 12 ( 2020-12), p. 1540-1551

Type of Medium: Online Resource

ISSN: 1529-2908 , 1529-2916

URL: Article

DOI: 10.1038/s41590-020-0793-3

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2026412-4

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Laurette, Patrick ; Strub, Thomas ; Koludrovic, Dana ; [et al.]

eLife Sciences Publications, Ltd ; 2015

In: eLife Vol. 4 ( 2015-03-24)

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In: eLife, eLife Sciences Publications, Ltd, Vol. 4 ( 2015-03-24)

Abstract: Melanocytes are pigment-producing cells found primarily in the skin. Many of the genes that help these cells to develop are also thought to affect the development of melanomas: an aggressive form of skin cancer that originates in these cells. One such gene encodes a protein called MITF. This protein binds to DNA and regulates genes that control the development, survival, and spread of melanocytes; it is also linked to the invasive properties of melanomas. The MITF protein works together with partner proteins to control numerous genes, activating some while inhibiting others, by binding to nearby stretches of DNA that act as regulatory elements. Its interactions are therefore widespread and complex. Now, Laurette, Strub et al. have used techniques called tandem affinity purification and mass spectrometry to identify the proteins that interact with MITF. This investigation found many new protein partners for MITF, including proteins involved in DNA damage, repair, and replication. MITF also associates with two proteins—one of which is called BRG1—that are involved in modifying how tightly DNA is packaged inside cells. DNA wrapped around proteins is known as chromatin, and if chromatin is tightly packed, the genes in that stretch of DNA cannot be easily accessed or activated. Removing BRG1 from melanocytes and melanoma cells caused the cells to die or stop growing. When BRG1 was removed from developing mouse embryos, melanocytes failed to form. Further investigation revealed that MITF, together with another protein, localize BRG1 to sites in the melanocyte's DNA to open up the chromatin and regulate nearby genes. Furthermore, Laurette, Strub et al. report that BRG1 binds to many such elements in a characteristic manner, in which two BRG1 proteins flank the stretch of DNA bound by MITF and several other key DNA-binding proteins that together regulate many aspects of melanocyte and melanoma cell physiology. Laurette, Strub et al. have therefore revealed many details about the molecules that activate genes in melanomas and melanocyte cells, as well as the interactions between these molecules. The results could also help researchers to understand how the BRG1 protein organises chromatin packing in other cell types.

Type of Medium: Online Resource

ISSN: 2050-084X

URL: Article

DOI: 10.7554/eLife.06857

DOI: 10.7554/eLife.06857.001

DOI: 10.7554/eLife.06857.002

DOI: 10.7554/eLife.06857.003

DOI: 10.7554/eLife.06857.004

DOI: 10.7554/eLife.06857.005

DOI: 10.7554/eLife.06857.006

DOI: 10.7554/eLife.06857.007

DOI: 10.7554/eLife.06857.008

DOI: 10.7554/eLife.06857.009

DOI: 10.7554/eLife.06857.010

DOI: 10.7554/eLife.06857.011

DOI: 10.7554/eLife.06857.012

DOI: 10.7554/eLife.06857.013

DOI: 10.7554/eLife.06857.014

DOI: 10.7554/eLife.06857.015

DOI: 10.7554/eLife.06857.016

DOI: 10.7554/eLife.06857.017

DOI: 10.7554/eLife.06857.018

DOI: 10.7554/eLife.06857.019

DOI: 10.7554/eLife.06857.020

DOI: 10.7554/eLife.06857.021

DOI: 10.7554/eLife.06857.022

DOI: 10.7554/eLife.06857.023

DOI: 10.7554/eLife.06857.024

DOI: 10.7554/eLife.06857.025

DOI: 10.7554/eLife.06857.026

Language: English

Publisher: eLife Sciences Publications, Ltd

Publication Date: 2015

detail.hit.zdb_id: 2687154-3

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Publisher Correction: Rational discovery of molecular glue degraders via scalable chemical profiling

Mayor-Ruiz, Cristina ; Bauer, Sophie ; Brand, Matthias ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Nature Chemical Biology Vol. 17, No. 3 ( 2021-03), p. 361-361

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In: Nature Chemical Biology, Springer Science and Business Media LLC, Vol. 17, No. 3 ( 2021-03), p. 361-361

Type of Medium: Online Resource

ISSN: 1552-4450 , 1552-4469

URL: Article

DOI: 10.1038/s41589-021-00735-4

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2190276-8

SSG: 12

SSG: 15,3

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Rational discovery of molecular glue degraders via scalable chemical profiling

Mayor-Ruiz, Cristina ; Bauer, Sophie ; Brand, Matthias ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Nature Chemical Biology Vol. 16, No. 11 ( 2020-11), p. 1199-1207

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In: Nature Chemical Biology, Springer Science and Business Media LLC, Vol. 16, No. 11 ( 2020-11), p. 1199-1207

Type of Medium: Online Resource

ISSN: 1552-4450 , 1552-4469

URL: Article

DOI: 10.1038/s41589-020-0594-x

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2190276-8

SSG: 12

SSG: 15,3

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Acute BAF perturbation causes immediate changes in chromatin accessibility

Schick, Sandra ; Grosche, Sarah ; Kohl, Katharina Eva ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Nature Genetics Vol. 53, No. 3 ( 2021-03), p. 269-278

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 53, No. 3 ( 2021-03), p. 269-278

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/s41588-021-00777-3

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 1494946-5

SSG: 12

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The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

Jacobs, Jelle ; Atkins, Mardelle ; Davie, Kristofer ; [et al.]

Springer Science and Business Media LLC ; 2018

In: Nature Genetics Vol. 50, No. 7 ( 2018-7), p. 1011-1020

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 50, No. 7 ( 2018-7), p. 1011-1020

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/s41588-018-0140-x

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 1494946-5

SSG: 12

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Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

Kalender Atak, Zeynep ; Imrichova, Hana ; Svetlichnyy, Dmitry ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Genome Medicine Vol. 9, No. 1 ( 2017-12)

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In: Genome Medicine, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2017-12)

Type of Medium: Online Resource

ISSN: 1756-994X

URL: Article

DOI: 10.1186/s13073-017-0464-7

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2484394-5

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Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

Verfaillie, Annelien ; Imrichova, Hana ; Atak, Zeynep Kalender ; [et al.]

Springer Science and Business Media LLC ; 2015

In: Nature Communications Vol. 6, No. 1 ( 2015-04-09)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2015-04-09)

Abstract: Transcriptional reprogramming of proliferative melanoma cells into a phenotypically distinct invasive cell subpopulation is a critical event at the origin of metastatic spreading. Here we generate transcriptome, open chromatin and histone modification maps of melanoma cultures; and integrate this data with existing transcriptome and DNA methylation profiles from tumour biopsies to gain insight into the mechanisms underlying this key reprogramming event. This shows thousands of genomic regulatory regions underlying the proliferative and invasive states, identifying SOX10/MITF and AP-1/TEAD as regulators, respectively. Knockdown of TEADs shows a previously unrecognized role in the invasive gene network and establishes a causative link between these transcription factors, cell invasion and sensitivity to MAPK inhibitors. Using regulatory landscapes and in silico analysis, we show that transcriptional reprogramming underlies the distinct cellular states present in melanoma. Furthermore, it reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/ncomms7683

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2015

detail.hit.zdb_id: 2553671-0

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i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Imrichová, Hana ; Hulselmans, Gert ; Kalender Atak, Zeynep ; [et al.]

Oxford University Press (OUP) ; 2015

In: Nucleic Acids Research Vol. 43, No. W1 ( 2015-07-01), p. W57-W64

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In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 43, No. W1 ( 2015-07-01), p. W57-W64

Type of Medium: Online Resource

ISSN: 0305-1048 , 1362-4962

URL: Article

DOI: 10.1093/nar/gkv395

RVK:

WA 15000

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2015

detail.hit.zdb_id: 1472175-2

SSG: 12

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iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

Janky, Rekin's ; Verfaillie, Annelien ; Imrichová, Hana ; [et al.]

Public Library of Science (PLoS) ; 2014

In: PLoS Computational Biology Vol. 10, No. 7 ( 2014-7-24), p. e1003731-

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In: PLoS Computational Biology, Public Library of Science (PLoS), Vol. 10, No. 7 ( 2014-7-24), p. e1003731-

Type of Medium: Online Resource

ISSN: 1553-7358

URL: Article

DOI: 10.1371/journal.pcbi.1003731

DOI: 10.1371/journal.pcbi.1003731.g001

DOI: 10.1371/journal.pcbi.1003731.g002

DOI: 10.1371/journal.pcbi.1003731.g003

DOI: 10.1371/journal.pcbi.1003731.g004

DOI: 10.1371/journal.pcbi.1003731.g005

DOI: 10.1371/journal.pcbi.1003731.g006

DOI: 10.1371/journal.pcbi.1003731.t001

DOI: 10.1371/journal.pcbi.1003731.s001

DOI: 10.1371/journal.pcbi.1003731.s002

DOI: 10.1371/journal.pcbi.1003731.s003

DOI: 10.1371/journal.pcbi.1003731.s004

DOI: 10.1371/journal.pcbi.1003731.s005

DOI: 10.1371/journal.pcbi.1003731.s006

DOI: 10.1371/journal.pcbi.1003731.s007

DOI: 10.1371/journal.pcbi.1003731.s008

DOI: 10.1371/journal.pcbi.1003731.s009

DOI: 10.1371/journal.pcbi.1003731.s010

DOI: 10.1371/journal.pcbi.1003731.s011

DOI: 10.1371/journal.pcbi.1003731.s012

DOI: 10.1371/journal.pcbi.1003731.s013

DOI: 10.1371/journal.pcbi.1003731.s014

DOI: 10.1371/journal.pcbi.1003731.s015

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2014

detail.hit.zdb_id: 2193340-6

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