---
_id: '11070'
abstract:
- lang: eng
  text: The organization of the genome in the three-dimensional space of the nucleus
    is coupled with cell type-specific gene expression. However, how nuclear architecture
    influences transcription that governs cell identity remains unknown. Here, we
    show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers
    (SE), regulatory structures that drive the expression of key genes that specify
    cell identity. We found that nucleoporin-associated SEs localize preferentially
    to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic
    transcriptional changes of SE-associated genes. Our results reveal a crucial role
    of NPC components in the regulation of cell type-specifying genes and highlight
    nuclear architecture as a regulatory layer of genome functions in cell fate.
article_processing_charge: No
article_type: original
author:
- first_name: Arkaitz
  full_name: Ibarra, Arkaitz
  last_name: Ibarra
- first_name: Chris
  full_name: Benner, Chris
  last_name: Benner
- first_name: Swati
  full_name: Tyagi, Swati
  last_name: Tyagi
- first_name: Jonah
  full_name: Cool, Jonah
  last_name: Cool
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. Nucleoporin-mediated regulation
    of cell identity genes. <i>Genes &#38; Development</i>. 2016;30(20):2253-2258.
    doi:<a href="https://doi.org/10.1101/gad.287417.116">10.1101/gad.287417.116</a>
  apa: Ibarra, A., Benner, C., Tyagi, S., Cool, J., &#38; Hetzer, M. (2016). Nucleoporin-mediated
    regulation of cell identity genes. <i>Genes &#38; Development</i>. Cold Spring
    Harbor Laboratory. <a href="https://doi.org/10.1101/gad.287417.116">https://doi.org/10.1101/gad.287417.116</a>
  chicago: Ibarra, Arkaitz, Chris Benner, Swati Tyagi, Jonah Cool, and Martin Hetzer.
    “Nucleoporin-Mediated Regulation of Cell Identity Genes.” <i>Genes &#38; Development</i>.
    Cold Spring Harbor Laboratory, 2016. <a href="https://doi.org/10.1101/gad.287417.116">https://doi.org/10.1101/gad.287417.116</a>.
  ieee: A. Ibarra, C. Benner, S. Tyagi, J. Cool, and M. Hetzer, “Nucleoporin-mediated
    regulation of cell identity genes,” <i>Genes &#38; Development</i>, vol. 30, no.
    20. Cold Spring Harbor Laboratory, pp. 2253–2258, 2016.
  ista: Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. 2016. Nucleoporin-mediated
    regulation of cell identity genes. Genes &#38; Development. 30(20), 2253–2258.
  mla: Ibarra, Arkaitz, et al. “Nucleoporin-Mediated Regulation of Cell Identity Genes.”
    <i>Genes &#38; Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory,
    2016, pp. 2253–58, doi:<a href="https://doi.org/10.1101/gad.287417.116">10.1101/gad.287417.116</a>.
  short: A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes &#38; Development
    30 (2016) 2253–2258.
date_created: 2022-04-07T07:48:08Z
date_published: 2016-11-02T00:00:00Z
date_updated: 2022-07-18T08:33:49Z
day: '02'
doi: 10.1101/gad.287417.116
extern: '1'
external_id:
  pmid:
  - '27807035'
intvolume: '        30'
issue: '20'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/gad.287417.116
month: '11'
oa: 1
oa_version: Published Version
page: 2253-2258
pmid: 1
publication: Genes & Development
publication_identifier:
  eissn:
  - 1549-5477
  issn:
  - 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleoporin-mediated regulation of cell identity genes
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 30
year: '2016'
...
---
_id: '11071'
abstract:
- lang: eng
  text: Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic
    cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic
    transport, recent research suggests that certain NPC proteins have additionally
    acquired the role of affecting gene expression at the nuclear periphery and in
    the nucleoplasm in metazoans. Here we identify a widely expressed variant of the
    transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that
    arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks
    the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead,
    sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified
    transcriptional regulator, at gene promoters to control transcription of its target
    genes in human cells. Interestingly, sPom121 transcripts appear independently
    in several mammalian species, suggesting convergent innovation of Nup-mediated
    transcription regulation during mammalian evolution. Our findings implicate alternate
    transcription initiation as a mechanism to increase the functional diversity of
    NPC components.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias M.
  full_name: Franks, Tobias M.
  last_name: Franks
- first_name: Chris
  full_name: Benner, Chris
  last_name: Benner
- first_name: Iñigo
  full_name: Narvaiza, Iñigo
  last_name: Narvaiza
- first_name: Maria C.N.
  full_name: Marchetto, Maria C.N.
  last_name: Marchetto
- first_name: Janet M.
  full_name: Young, Janet M.
  last_name: Young
- first_name: Harmit S.
  full_name: Malik, Harmit S.
  last_name: Malik
- first_name: Fred H.
  full_name: Gage, Fred H.
  last_name: Gage
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Franks TM, Benner C, Narvaiza I, et al. Evolution of a transcriptional regulator
    from a transmembrane nucleoporin. <i>Genes &#38; Development</i>. 2016;30(10):1155-1171.
    doi:<a href="https://doi.org/10.1101/gad.280941.116">10.1101/gad.280941.116</a>
  apa: Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C. N., Young, J. M.,
    Malik, H. S., … Hetzer, M. (2016). Evolution of a transcriptional regulator from
    a transmembrane nucleoporin. <i>Genes &#38; Development</i>. Cold Spring Harbor
    Laboratory. <a href="https://doi.org/10.1101/gad.280941.116">https://doi.org/10.1101/gad.280941.116</a>
  chicago: Franks, Tobias M., Chris Benner, Iñigo Narvaiza, Maria C.N. Marchetto,
    Janet M. Young, Harmit S. Malik, Fred H. Gage, and Martin Hetzer. “Evolution of
    a Transcriptional Regulator from a Transmembrane Nucleoporin.” <i>Genes &#38;
    Development</i>. Cold Spring Harbor Laboratory, 2016. <a href="https://doi.org/10.1101/gad.280941.116">https://doi.org/10.1101/gad.280941.116</a>.
  ieee: T. M. Franks <i>et al.</i>, “Evolution of a transcriptional regulator from
    a transmembrane nucleoporin,” <i>Genes &#38; Development</i>, vol. 30, no. 10.
    Cold Spring Harbor Laboratory, pp. 1155–1171, 2016.
  ista: Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH,
    Hetzer M. 2016. Evolution of a transcriptional regulator from a transmembrane
    nucleoporin. Genes &#38; Development. 30(10), 1155–1171.
  mla: Franks, Tobias M., et al. “Evolution of a Transcriptional Regulator from a
    Transmembrane Nucleoporin.” <i>Genes &#38; Development</i>, vol. 30, no. 10, Cold
    Spring Harbor Laboratory, 2016, pp. 1155–71, doi:<a href="https://doi.org/10.1101/gad.280941.116">10.1101/gad.280941.116</a>.
  short: T.M. Franks, C. Benner, I. Narvaiza, M.C.N. Marchetto, J.M. Young, H.S. Malik,
    F.H. Gage, M. Hetzer, Genes &#38; Development 30 (2016) 1155–1171.
date_created: 2022-04-07T07:48:20Z
date_published: 2016-05-19T00:00:00Z
date_updated: 2022-07-18T08:33:50Z
day: '19'
doi: 10.1101/gad.280941.116
extern: '1'
external_id:
  pmid:
  - '27198230'
intvolume: '        30'
issue: '10'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/gad.280941.116
month: '05'
oa: 1
oa_version: Published Version
page: 1155-1171
pmid: 1
publication: Genes & Development
publication_identifier:
  eissn:
  - 1549-5477
  issn:
  - 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of a transcriptional regulator from a transmembrane nucleoporin
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 30
year: '2016'
...
---
_id: '11076'
abstract:
- lang: eng
  text: Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different
    proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE)
    and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this
    vital role, NPC components influence genome functions in a transport-independent
    manner. Nups play an evolutionarily conserved role in gene expression regulation
    that, in metazoans, extends into the nuclear interior. Additionally, in proliferative
    cells, Nups play a crucial role in genome integrity maintenance and mitotic progression.
    Here we discuss genome-related functions of Nups and their impact on essential
    DNA metabolism processes such as transcription, chromosome duplication, and segregation.
article_processing_charge: No
article_type: original
author:
- first_name: Arkaitz
  full_name: Ibarra, Arkaitz
  last_name: Ibarra
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Ibarra A, Hetzer M. Nuclear pore proteins and the control of genome functions.
    <i>Genes &#38; Development</i>. 2015;29(4):337-349. doi:<a href="https://doi.org/10.1101/gad.256495.114">10.1101/gad.256495.114</a>
  apa: Ibarra, A., &#38; Hetzer, M. (2015). Nuclear pore proteins and the control
    of genome functions. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory.
    <a href="https://doi.org/10.1101/gad.256495.114">https://doi.org/10.1101/gad.256495.114</a>
  chicago: Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control
    of Genome Functions.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory,
    2015. <a href="https://doi.org/10.1101/gad.256495.114">https://doi.org/10.1101/gad.256495.114</a>.
  ieee: A. Ibarra and M. Hetzer, “Nuclear pore proteins and the control of genome
    functions,” <i>Genes &#38; Development</i>, vol. 29, no. 4. Cold Spring Harbor
    Laboratory, pp. 337–349, 2015.
  ista: Ibarra A, Hetzer M. 2015. Nuclear pore proteins and the control of genome
    functions. Genes &#38; Development. 29(4), 337–349.
  mla: Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control
    of Genome Functions.” <i>Genes &#38; Development</i>, vol. 29, no. 4, Cold Spring
    Harbor Laboratory, 2015, pp. 337–49, doi:<a href="https://doi.org/10.1101/gad.256495.114">10.1101/gad.256495.114</a>.
  short: A. Ibarra, M. Hetzer, Genes &#38; Development 29 (2015) 337–349.
date_created: 2022-04-07T07:49:21Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2022-07-18T08:43:20Z
day: '01'
doi: 10.1101/gad.256495.114
extern: '1'
external_id:
  pmid:
  - '25691464'
intvolume: '        29'
issue: '4'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/gad.256495.114
month: '02'
oa: 1
oa_version: Published Version
page: 337-349
pmid: 1
publication: Genes & Development
publication_identifier:
  eissn:
  - 1549-5477
  issn:
  - 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear pore proteins and the control of genome functions
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 29
year: '2015'
...
---
_id: '11077'
abstract:
- lang: eng
  text: Nucleoporins (Nups) are a family of proteins best known as the constituent
    building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that
    mediate nuclear transport across the nuclear envelope. Recent evidence suggests
    that several Nups have additional roles in controlling the activation and silencing
    of developmental genes; however, the mechanistic details of these functions remain
    poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem
    cells (mESCs) causes the derepression of developmental genes and induction of
    early differentiation. This loss of stem cell identity is not associated with
    defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds
    around the transcriptional start site (TSS) of developmental genes and mediates
    the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its
    target loci. Our results demonstrate a chromatin-associated role of Nup153 in
    maintaining stem cell pluripotency by functioning in mammalian epigenetic gene
    silencing.
article_processing_charge: No
article_type: original
author:
- first_name: Filipe V.
  full_name: Jacinto, Filipe V.
  last_name: Jacinto
- first_name: Chris
  full_name: Benner, Chris
  last_name: Benner
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Jacinto FV, Benner C, Hetzer M. The nucleoporin Nup153 regulates embryonic
    stem cell pluripotency through gene silencing. <i>Genes &#38; Development</i>.
    2015;29(12):1224-1238. doi:<a href="https://doi.org/10.1101/gad.260919.115">10.1101/gad.260919.115</a>
  apa: Jacinto, F. V., Benner, C., &#38; Hetzer, M. (2015). The nucleoporin Nup153
    regulates embryonic stem cell pluripotency through gene silencing. <i>Genes &#38;
    Development</i>. Cold Spring Harbor Laboratory. <a href="https://doi.org/10.1101/gad.260919.115">https://doi.org/10.1101/gad.260919.115</a>
  chicago: Jacinto, Filipe V., Chris Benner, and Martin Hetzer. “The Nucleoporin Nup153
    Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” <i>Genes &#38;
    Development</i>. Cold Spring Harbor Laboratory, 2015. <a href="https://doi.org/10.1101/gad.260919.115">https://doi.org/10.1101/gad.260919.115</a>.
  ieee: F. V. Jacinto, C. Benner, and M. Hetzer, “The nucleoporin Nup153 regulates
    embryonic stem cell pluripotency through gene silencing,” <i>Genes &#38; Development</i>,
    vol. 29, no. 12. Cold Spring Harbor Laboratory, pp. 1224–1238, 2015.
  ista: Jacinto FV, Benner C, Hetzer M. 2015. The nucleoporin Nup153 regulates embryonic
    stem cell pluripotency through gene silencing. Genes &#38; Development. 29(12),
    1224–1238.
  mla: Jacinto, Filipe V., et al. “The Nucleoporin Nup153 Regulates Embryonic Stem
    Cell Pluripotency through Gene Silencing.” <i>Genes &#38; Development</i>, vol.
    29, no. 12, Cold Spring Harbor Laboratory, 2015, pp. 1224–38, doi:<a href="https://doi.org/10.1101/gad.260919.115">10.1101/gad.260919.115</a>.
  short: F.V. Jacinto, C. Benner, M. Hetzer, Genes &#38; Development 29 (2015) 1224–1238.
date_created: 2022-04-07T07:49:31Z
date_published: 2015-06-16T00:00:00Z
date_updated: 2022-07-18T08:43:51Z
day: '16'
doi: 10.1101/gad.260919.115
extern: '1'
external_id:
  pmid:
  - '26080816'
intvolume: '        29'
issue: '12'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/gad.260919.115
month: '06'
oa: 1
oa_version: Published Version
page: 1224-1238
pmid: 1
publication: Genes & Development
publication_identifier:
  eissn:
  - 1549-5477
  issn:
  - 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene
  silencing
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 29
year: '2015'
...
---
_id: '9532'
abstract:
- lang: eng
  text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
    of origin-dependent gene expression, is observed in mammals and flowering plants.
    Genome-scale surveys of imprinted expression and the underlying differential epigenetic
    marks have led to the discovery of hundreds of imprinted plant genes and confirmed
    DNA and histone methylation as key regulators of plant imprinting. However, the
    biological roles of the vast majority of imprinted plant genes are unknown, and
    the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
    review the mechanisms of plant genomic imprinting and discuss theories of imprinting
    evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
  full_name: Rodrigues, Jessica A.
  last_name: Rodrigues
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
    plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href="https://doi.org/10.1101/gad.269902.115">10.1101/gad.269902.115</a>
  apa: Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic
    imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory
    Press. <a href="https://doi.org/10.1101/gad.269902.115">https://doi.org/10.1101/gad.269902.115</a>
  chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
    Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor
    Laboratory Press, 2015. <a href="https://doi.org/10.1101/gad.269902.115">https://doi.org/10.1101/gad.269902.115</a>.
  ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
    in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor
    Laboratory Press, pp. 2517–2531, 2015.
  ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
    in plants. Genes and Development. 29(24), 2517–2531.
  mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
    Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring
    Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href="https://doi.org/10.1101/gad.269902.115">10.1101/gad.269902.115</a>.
  short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-12-14T07:58:15Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1101/gad.269902.115
extern: '1'
external_id:
  pmid:
  - '26680300'
file:
- access_level: open_access
  checksum: 086a88cfca4677646da26ed960cb02e9
  content_type: application/pdf
  creator: asandaue
  date_created: 2021-06-08T09:55:10Z
  date_updated: 2021-06-08T09:55:10Z
  file_id: '9533'
  file_name: 2015_GenesAndDevelopment_Rodrigues.pdf
  file_size: 1116846
  relation: main_file
  success: 1
file_date_updated: 2021-06-08T09:55:10Z
has_accepted_license: '1'
intvolume: '        29'
issue: '24'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 2517–2531
pmid: 1
publication: Genes and Development
publication_identifier:
  eissn:
  - 1549-5477
  issn:
  - 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution and function of genomic imprinting in plants
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 29
year: '2015'
...