---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21983'
abstract:
- lang: eng
  text: 'Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences
    that bind transcription factor (TF) proteins to up- or down-regulate target genes.
    Decades-long efforts yielded TF-DNA interaction models that predict how strongly
    an individual TF binds arbitrary DNA sequences and how individual binding events
    on the CRE combine to affect gene expression. These insights can be synthesized
    into a global, biophysically realistic, and quantitative genotype–phenotype map
    for gene regulation, a ‘holy grail’ for the application of evolutionary theory.
    A global map provides a rare opportunity to simulate the long-term evolution of
    regulatory sequences and pose several fundamental questions: How long does it
    take to evolve CREs de novo? How many non-trivial regulatory functions exist in
    sequence space? How connected are they? For which regulatory architecture is CRE
    evolution most rapid and evolvable? In this article, the first of a two-part series,
    we briefly review the pertinent modeling and simulation efforts for a unique system
    that enables close, quantitative, and mechanistic links between biophysics, as
    well as systems, synthetic, and evolutionary biology.'
acknowledgement: "We thank Nick Barton and Noa Ottilie Borst for essential contributions
  to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship,
  jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science
  and Technology Austria (ISTA).\r\nThis study was supported by the European Molecular
  Biology Laboratory (J.C.); the European Molecular Biology Laboratory Interdisciplinary
  Postdoc Programme (EIPOD) under the Marie Skłodowska-Curie Actions cofund (S.H.A.)."
article_number: '102483'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Elia
  full_name: Mascolo, Elia
  id: 776a6ed0-a053-11f0-8635-80b95e0e0d53
  last_name: Mascolo
  orcid: 0000-0003-2977-7844
- first_name: Reka E
  full_name: Körei, Reka E
  id: 50FDE43E-AA30-11E9-A72B-8A12E6697425
  last_name: Körei
- first_name: Santiago
  full_name: Herrera-Álvarez, Santiago
  last_name: Herrera-Álvarez
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Justin
  full_name: Crocker, Justin
  last_name: Crocker
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
citation:
  ama: 'Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. Long-term
    evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic
    genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>.
    2026;99. doi:<a href="https://doi.org/10.1016/j.gde.2026.102483">10.1016/j.gde.2026.102483</a>'
  apa: 'Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., Crocker, J.,
    &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part
    1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current
    Opinion in Genetics &#38; Development</i>. Elsevier. <a href="https://doi.org/10.1016/j.gde.2026.102483">https://doi.org/10.1016/j.gde.2026.102483</a>'
  chicago: 'Mascolo, Elia, Reka E Körei, Santiago Herrera-Álvarez, Calin C Guet, Justin
    Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences.
    Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.”
    <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2026. <a href="https://doi.org/10.1016/j.gde.2026.102483">https://doi.org/10.1016/j.gde.2026.102483</a>.'
  ieee: 'E. Mascolo, R. E. Körei, S. Herrera-Álvarez, C. C. Guet, J. Crocker, and
    G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 1: Simulations
    on global, biophysically-realistic genotype–phenotype maps,” <i>Current Opinion
    in Genetics &#38; Development</i>, vol. 99. Elsevier, 2026.'
  ista: 'Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. 2026.
    Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global,
    biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics &#38;
    Development. 99, 102483.'
  mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part
    1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current
    Opinion in Genetics &#38; Development</i>, vol. 99, 102483, Elsevier, 2026, doi:<a
    href="https://doi.org/10.1016/j.gde.2026.102483">10.1016/j.gde.2026.102483</a>.'
  short: E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik,
    Current Opinion in Genetics &#38; Development 99 (2026).
corr_author: '1'
date_created: 2026-06-10T07:37:12Z
date_published: 2026-05-09T00:00:00Z
date_updated: 2026-06-16T12:37:02Z
day: '09'
ddc:
- '570'
department:
- _id: GradSch
- _id: CaGu
- _id: GaTk
doi: 10.1016/j.gde.2026.102483
external_id:
  arxiv:
  - '2601.19681'
has_accepted_license: '1'
intvolume: '        99'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.gde.2026.102483
month: '05'
oa: 1
oa_version: Published Version
publication: Current Opinion in Genetics & Development
publication_identifier:
  eissn:
  - 1879-0380
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global,
  biophysically-realistic genotype–phenotype maps'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21759'
abstract:
- lang: eng
  text: 'Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences
    that bind transcription factor (TF) proteins to up- or down-regulate target genes.
    Decades-long efforts yielded TF-DNA interaction models that predict how strongly
    an individual TF binds arbitrary DNA sequences and how individual binding events
    on the CRE combine to affect gene expression. These insights can be synthesized
    into a global, biophysically realistic, and quantitative genotype-phenotype (GP)
    map for gene regulation, a ‘holy grail’ for the application of evolutionary theory.
    A global map provides a rare opportunity to simulate the long-term evolution of
    regulatory sequences and pose several fundamental questions: How long does it
    take to evolve CREs de novo? How many non-trivial regulatory functions exist in
    sequence space? How connected are they? For which regulatory architecture is CRE
    evolution most rapid and evolvable? In this article, the second of a two-part
    series, we review the application of evolutionary concepts — epistasis, robustness,
    evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene
    regulatory sequences. We then evaluate the potential for a unifying theory for
    the evolution of regulatory sequences and identify key open challenges.'
acknowledgement: "We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions
  to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship,
  jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science
  and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant
  101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European
  Molecular Biology Laboratory (N.O.B., J.C.)."
article_number: '102472'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Elia
  full_name: Mascolo, Elia
  id: 776a6ed0-a053-11f0-8635-80b95e0e0d53
  last_name: Mascolo
  orcid: 0000-0003-2977-7844
- first_name: Reka E
  full_name: Körei, Reka E
  id: 50FDE43E-AA30-11E9-A72B-8A12E6697425
  last_name: Körei
- first_name: Noa O.
  full_name: Borst, Noa O.
  last_name: Borst
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
- first_name: Justin
  full_name: Crocker, Justin
  last_name: Crocker
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
citation:
  ama: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution
    of regulatory DNA sequences. Part 2: Theory and future challenges. <i>Current
    Opinion in Genetics &#38; Development</i>. 2026;98. doi:<a href="https://doi.org/10.1016/j.gde.2026.102472">10.1016/j.gde.2026.102472</a>'
  apa: 'Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., &#38;
    Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory
    and future challenges. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.gde.2026.102472">https://doi.org/10.1016/j.gde.2026.102472</a>'
  chicago: 'Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker,
    and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory
    and Future Challenges.” <i>Current Opinion in Genetics &#38; Development</i>.
    Elsevier, 2026. <a href="https://doi.org/10.1016/j.gde.2026.102472">https://doi.org/10.1016/j.gde.2026.102472</a>.'
  ieee: 'E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik,
    “Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,”
    <i>Current Opinion in Genetics &#38; Development</i>, vol. 98. Elsevier, 2026.'
  ista: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term
    evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current
    Opinion in Genetics &#38; Development. 98, 102472.'
  mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part
    2: Theory and Future Challenges.” <i>Current Opinion in Genetics &#38; Development</i>,
    vol. 98, 102472, Elsevier, 2026, doi:<a href="https://doi.org/10.1016/j.gde.2026.102472">10.1016/j.gde.2026.102472</a>.'
  short: E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current
    Opinion in Genetics &#38; Development 98 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: No data were used for the research described in the article.
date_created: 2026-04-26T22:01:46Z
date_published: 2026-06-01T00:00:00Z
date_updated: 2026-08-12T09:56:02Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1016/j.gde.2026.102472
file:
- access_level: open_access
  checksum: ac8bbee61717bfe7116e312cc6825259
  content_type: application/pdf
  creator: dernst
  date_created: 2026-07-27T13:39:59Z
  date_updated: 2026-07-27T13:39:59Z
  file_id: '22590'
  file_name: 2026_CurrentOpinionGeneticsDev_Mascolo.pdf
  file_size: 3190001
  relation: main_file
  success: 1
file_date_updated: 2026-07-27T13:39:59Z
has_accepted_license: '1'
intvolume: '        98'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
  grant_number: '101055327'
  name: Understanding the evolution of continuous genomes
publication: Current Opinion in Genetics & Development
publication_identifier:
  eissn:
  - 1879-0380
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Long-term evolution of regulatory DNA sequences. Part 2: Theory and future
  challenges'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21948'
abstract:
- lang: eng
  text: The cerebral cortex comprises diverse neuron and glial cell types generated
    by radial glial progenitors (RGPs) during development. Although RGPs broadly differentiate
    according to temporally and spatially regulated molecular logics, the lineage
    hierarchies linking individual progenitors to defined cell (sub)types are not
    well understood. Clone-resolved transcriptomics, combining molecular barcoding
    and single-cell RNA sequencing, allow high-resolution lineage tracing at the single-clone/cell
    level across different species and models. In this mini-review, we synthesize
    recent advances in this field, uncovering unexpected lineage relationships in
    the developing brain, with a particular focus on the cerebral cortex. We further
    highlight new insights into species-specific differences in the developmental
    programs generating cell-type diversity, linking changes in clonal architecture
    to lineage diversification during cortical evolution.
acknowledgement: We wish to thank all members of the Hippenmeyer laboratory at ISTA
  for exciting discussions on the subject of this review. We apologize to colleagues
  whose work we could not cite and/or discuss in the frame of the available space.
  Work in the Hippenmeyer laboratory on the discussed topic is supported by ISTA institutional
  funds, an EMBO LTF (ALTF 994–2023) to F.P., FWF SFB F78 (10.55776/F78) to S.H.,
  and FWF Cluster of Excellence COE16 (10.55776/COE16) to S.H.
article_number: '102487'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Irene
  full_name: Varela Martínez, Irene
  id: a69b5985-8829-11f0-8fc2-d0af58f64471
  last_name: Varela Martínez
- first_name: Fabrizia
  full_name: Pipicelli, Fabrizia
  id: 649134fd-d012-11ed-8f82-db1e5050f9ba
  last_name: Pipicelli
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: 'Varela Martínez I, Pipicelli F, Hippenmeyer S. Tracing cell lineages in the
    developing brain: Insights from mosaic analysis and clone-resolved transcriptomics.
    <i>Current Opinion in Genetics &#38; Development</i>. 2026;99. doi:<a href="https://doi.org/10.1016/j.gde.2026.102487">10.1016/j.gde.2026.102487</a>'
  apa: 'Varela Martínez, I., Pipicelli, F., &#38; Hippenmeyer, S. (2026). Tracing
    cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved
    transcriptomics. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.gde.2026.102487">https://doi.org/10.1016/j.gde.2026.102487</a>'
  chicago: 'Varela Martínez, Irene, Fabrizia Pipicelli, and Simon Hippenmeyer. “Tracing
    Cell Lineages in the Developing Brain: Insights from Mosaic Analysis and Clone-Resolved
    Transcriptomics.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier,
    2026. <a href="https://doi.org/10.1016/j.gde.2026.102487">https://doi.org/10.1016/j.gde.2026.102487</a>.'
  ieee: 'I. Varela Martínez, F. Pipicelli, and S. Hippenmeyer, “Tracing cell lineages
    in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics,”
    <i>Current Opinion in Genetics &#38; Development</i>, vol. 99. Elsevier, 2026.'
  ista: 'Varela Martínez I, Pipicelli F, Hippenmeyer S. 2026. Tracing cell lineages
    in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics.
    Current Opinion in Genetics &#38; Development. 99, 102487.'
  mla: 'Varela Martínez, Irene, et al. “Tracing Cell Lineages in the Developing Brain:
    Insights from Mosaic Analysis and Clone-Resolved Transcriptomics.” <i>Current
    Opinion in Genetics &#38; Development</i>, vol. 99, 102487, Elsevier, 2026, doi:<a
    href="https://doi.org/10.1016/j.gde.2026.102487">10.1016/j.gde.2026.102487</a>.'
  short: I. Varela Martínez, F. Pipicelli, S. Hippenmeyer, Current Opinion in Genetics
    &#38; Development 99 (2026).
corr_author: '1'
date_created: 2026-06-07T22:01:35Z
date_published: 2026-05-29T00:00:00Z
date_updated: 2026-08-12T09:56:19Z
day: '29'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.gde.2026.102487
external_id:
  pmid:
  - '42214837'
has_accepted_license: '1'
intvolume: '        99'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.gde.2026.102487
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7c084566-9f16-11ee-852c-c88a1dbbf1cf
  grant_number: ALTF 994-2023
  name: Role of cell lineage in generating cell-type diversity in developing neocortex’
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
  grant_number: F7805
  name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
    Mechanisms of Neural Stem Cell Lineage Progression
publication: Current Opinion in Genetics & Development
publication_identifier:
  eissn:
  - 1879-0380
  issn:
  - 0959-437X
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tracing cell lineages in the developing brain: Insights from mosaic analysis
  and clone-resolved transcriptomics'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2026'
...
---
_id: '13965'
abstract:
- lang: eng
  text: Many modes and mechanisms of epigenetic inheritance have been elucidated in
    eukaryotes. Most of them are relatively short-term, generally not exceeding one
    or a few organismal generations. However, emerging evidence indicates that one
    mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much
    longer timescales, which are mostly or completely inaccessible in the laboratory.
    Here we discuss the evidence for, and mechanisms and implications of, such long-term
    epigenetic inheritance. We argue that compelling evidence supports the long-term
    epigenetic inheritance of gene body methylation, at least in the model angiosperm
    Arabidopsis thaliana, and that variation in such methylation can therefore serve
    as an epigenetic basis for phenotypic variation in natural populations.
article_number: '102087'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Elizabeth
  full_name: Hollwey, Elizabeth
  id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
  last_name: Hollwey
- first_name: Amy
  full_name: Briffa, Amy
  last_name: Briffa
- first_name: Martin
  full_name: Howard, Martin
  last_name: Howard
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications
    of long-term epigenetic inheritance. <i>Current Opinion in Genetics &#38; Development</i>.
    2023;81(8). doi:<a href="https://doi.org/10.1016/j.gde.2023.102087">10.1016/j.gde.2023.102087</a>
  apa: Hollwey, E., Briffa, A., Howard, M., &#38; Zilberman, D. (2023). Concepts,
    mechanisms and implications of long-term epigenetic inheritance. <i>Current Opinion
    in Genetics &#38; Development</i>. Elsevier. <a href="https://doi.org/10.1016/j.gde.2023.102087">https://doi.org/10.1016/j.gde.2023.102087</a>
  chicago: Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts,
    Mechanisms and Implications of Long-Term Epigenetic Inheritance.” <i>Current Opinion
    in Genetics &#38; Development</i>. Elsevier, 2023. <a href="https://doi.org/10.1016/j.gde.2023.102087">https://doi.org/10.1016/j.gde.2023.102087</a>.
  ieee: E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms
    and implications of long-term epigenetic inheritance,” <i>Current Opinion in Genetics
    &#38; Development</i>, vol. 81, no. 8. Elsevier, 2023.
  ista: Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and
    implications of long-term epigenetic inheritance. Current Opinion in Genetics
    &#38; Development. 81(8), 102087.
  mla: Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term
    Epigenetic Inheritance.” <i>Current Opinion in Genetics &#38; Development</i>,
    vol. 81, no. 8, 102087, Elsevier, 2023, doi:<a href="https://doi.org/10.1016/j.gde.2023.102087">10.1016/j.gde.2023.102087</a>.
  short: E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics
    &#38; Development 81 (2023).
corr_author: '1'
date_created: 2023-08-06T22:01:10Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-08-12T09:55:32Z
day: '01'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.gde.2023.102087
external_id:
  isi:
  - '001047020200001'
  pmid:
  - '37441873'
file:
- access_level: open_access
  checksum: a294cd9506b80ed6ef218ef44ed32765
  content_type: application/pdf
  creator: dernst
  date_created: 2023-08-07T08:32:26Z
  date_updated: 2023-08-07T08:32:26Z
  file_id: '13980'
  file_name: 2023_CurrentOpinionGenetics_Hollwey.pdf
  file_size: 2568632
  relation: main_file
  success: 1
file_date_updated: 2023-08-07T08:32:26Z
has_accepted_license: '1'
intvolume: '        81'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Genetics & Development
publication_identifier:
  eissn:
  - 1879-0380
  issn:
  - 0959-437X
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concepts, mechanisms and implications of long-term epigenetic inheritance
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2023'
...
---
_id: '8131'
abstract:
- lang: eng
  text: The possibility to generate construct valid animal models enabled the development
    and testing of therapeutic strategies targeting the core features of autism spectrum
    disorders (ASDs). At the same time, these studies highlighted the necessity of
    identifying sensitive developmental time windows for successful therapeutic interventions.
    Animal and human studies also uncovered the possibility to stratify the variety
    of ASDs in molecularly distinct subgroups, potentially facilitating effective
    treatment design. Here, we focus on the molecular pathways emerging as commonly
    affected by mutations in diverse ASD-risk genes, on their role during critical
    windows of brain development and the potential treatments targeting these biological
    processes.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bernadette
  full_name: Basilico, Bernadette
  id: 36035796-5ACA-11E9-A75E-7AF2E5697425
  last_name: Basilico
  orcid: 0000-0003-1843-3173
- first_name: Jasmin
  full_name: Morandell, Jasmin
  id: 4739D480-F248-11E8-B48F-1D18A9856A87
  last_name: Morandell
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
citation:
  ama: Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD
    treatments. <i>Current Opinion in Genetics &#38; Development</i>. 2020;65(12):126-137.
    doi:<a href="https://doi.org/10.1016/j.gde.2020.06.004">10.1016/j.gde.2020.06.004</a>
  apa: Basilico, B., Morandell, J., &#38; Novarino, G. (2020). Molecular mechanisms
    for targeted ASD treatments. <i>Current Opinion in Genetics &#38; Development</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.gde.2020.06.004">https://doi.org/10.1016/j.gde.2020.06.004</a>
  chicago: Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms
    for Targeted ASD Treatments.” <i>Current Opinion in Genetics &#38; Development</i>.
    Elsevier, 2020. <a href="https://doi.org/10.1016/j.gde.2020.06.004">https://doi.org/10.1016/j.gde.2020.06.004</a>.
  ieee: B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted
    ASD treatments,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 65,
    no. 12. Elsevier, pp. 126–137, 2020.
  ista: Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted
    ASD treatments. Current Opinion in Genetics &#38; Development. 65(12), 126–137.
  mla: Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.”
    <i>Current Opinion in Genetics &#38; Development</i>, vol. 65, no. 12, Elsevier,
    2020, pp. 126–37, doi:<a href="https://doi.org/10.1016/j.gde.2020.06.004">10.1016/j.gde.2020.06.004</a>.
  short: B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics &#38;
    Development 65 (2020) 126–137.
corr_author: '1'
date_created: 2020-07-19T22:00:58Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2026-08-17T22:31:11Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.gde.2020.06.004
ec_funded: 1
external_id:
  isi:
  - '000598918900019'
  pmid:
  - '32659636'
file:
- access_level: open_access
  content_type: application/pdf
  creator: dernst
  date_created: 2020-07-22T06:47:45Z
  date_updated: 2020-07-22T06:47:45Z
  file_id: '8146'
  file_name: 2020_CurrentOpGenetics_Basilico.pdf
  file_size: 1381545
  relation: main_file
  success: 1
file_date_updated: 2020-07-22T06:47:45Z
has_accepted_license: '1'
intvolume: '        65'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 126-137
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
  grant_number: F7807
  name: Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem
    cells in autism and epilepsy
publication: Current Opinion in Genetics & Development
publication_identifier:
  eissn:
  - 1879-0380
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '8620'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Molecular mechanisms for targeted ASD treatments
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 65
year: '2020'
...
---
_id: '1004'
abstract:
- lang: eng
  text: The fundamental tasks of the root system are, besides anchoring, mediating
    interactions between plant and soil and providing the plant with water and nutrients.
    The architecture of the root system is controlled by endogenous mechanisms that
    constantly integrate environmental signals, such as availability of nutrients
    and water. Extremely important for efficient soil exploitation and survival under
    less favorable conditions is the developmental flexibility of the root system
    that is largely determined by its postembryonic branching capacity. Modulation
    of initiation and outgrowth of lateral roots provides roots with an exceptional
    plasticity, allows optimal adjustment to underground heterogeneity, and enables
    effective soil exploitation and use of resources. Here we discuss recent advances
    in understanding the molecular mechanisms that shape the plant root system and
    integrate external cues to adapt to the changing environment.
article_processing_charge: No
author:
- first_name: Krisztina
  full_name: Ötvös, Krisztina
  id: 29B901B0-F248-11E8-B48F-1D18A9856A87
  last_name: Ötvös
  orcid: 0000-0002-5503-4983
- first_name: Eva
  full_name: Benková, Eva
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
citation:
  ama: Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. <i>Current
    Opinion in Genetics &#38; Development</i>. 2017;45:82-89. doi:<a href="https://doi.org/10.1016/j.gde.2017.03.010">10.1016/j.gde.2017.03.010</a>
  apa: Ötvös, K., &#38; Benková, E. (2017). Spatiotemporal mechanisms of root branching.
    <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href="https://doi.org/10.1016/j.gde.2017.03.010">https://doi.org/10.1016/j.gde.2017.03.010</a>
  chicago: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
    <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2017. <a href="https://doi.org/10.1016/j.gde.2017.03.010">https://doi.org/10.1016/j.gde.2017.03.010</a>.
  ieee: K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” <i>Current
    Opinion in Genetics &#38; Development</i>, vol. 45. Elsevier, pp. 82–89, 2017.
  ista: Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current
    Opinion in Genetics &#38; Development. 45, 82–89.
  mla: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
    <i>Current Opinion in Genetics &#38; Development</i>, vol. 45, Elsevier, 2017,
    pp. 82–89, doi:<a href="https://doi.org/10.1016/j.gde.2017.03.010">10.1016/j.gde.2017.03.010</a>.
  short: K. Ötvös, E. Benková, Current Opinion in Genetics &#38; Development 45 (2017)
    82–89.
date_created: 2018-12-11T11:49:38Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2026-04-16T09:56:36Z
day: '01'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1016/j.gde.2017.03.010
external_id:
  isi:
  - '000404880400013'
  pmid:
  - '28391060'
file:
- access_level: open_access
  content_type: application/pdf
  creator: dernst
  date_created: 2019-04-17T08:00:36Z
  date_updated: 2019-04-17T08:00:36Z
  file_id: '6336'
  file_name: Otvos_Benkova_CurOpDevBiol_2017.pdf
  file_size: 364133
  relation: main_file
  success: 1
file_date_updated: 2019-04-17T08:00:36Z
has_accepted_license: '1'
intvolume: '        45'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 82 - 89
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I 1774-B16
  name: Hormone cross-talk drives nutrient dependent plant development
publication: Current Opinion in Genetics & Development
publication_identifier:
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
publist_id: '6394'
pubrep_id: '1017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatiotemporal mechanisms of root branching
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 45
year: '2017'
...
---
_id: '9528'
abstract:
- lang: eng
  text: Accumulating evidence points toward diverse functions for plant chromatin.
    Remarkable progress has been made over the last few years in elucidating the mechanisms
    for a number of these functions. Activity of the histone demethylase IBM1 accurately
    targets DNA methylation to silent repeats and transposable elements, not to genes.
    A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes
    in sensing precise differences in ambient temperature and consequent gene regulation.
    Precise maintenance of chromosome number is assured by a histone modification
    that suppresses inappropriate DNA replication and by centromeric histone H3 regulation
    of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS
    C, the expression of which quantitatively measures the duration of cold exposure,
    functioning as memory of winter. These findings are a testament to the power of
    using plants to research chromatin organization, and demonstrate examples of how
    chromatin functions to achieve biological accuracy, precision, and memory.
article_processing_charge: No
article_type: review
author:
- first_name: Jason T.
  full_name: Huff, Jason T.
  last_name: Huff
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory
    by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>.
    2012;22(2):132-138. doi:<a href="https://doi.org/10.1016/j.gde.2012.01.007">10.1016/j.gde.2012.01.007</a>
  apa: Huff, J. T., &#38; Zilberman, D. (2012). Regulation of biological accuracy,
    precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics
    and Development</i>. Elsevier. <a href="https://doi.org/10.1016/j.gde.2012.01.007">https://doi.org/10.1016/j.gde.2012.01.007</a>
  chicago: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy,
    Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in
    Genetics and Development</i>. Elsevier, 2012. <a href="https://doi.org/10.1016/j.gde.2012.01.007">https://doi.org/10.1016/j.gde.2012.01.007</a>.
  ieee: J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision,
    and memory by plant chromatin organization,” <i>Current Opinion in Genetics and
    Development</i>, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.
  ista: Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision,
    and memory by plant chromatin organization. Current Opinion in Genetics and Development.
    22(2), 132–138.
  mla: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision,
    and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and
    Development</i>, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:<a href="https://doi.org/10.1016/j.gde.2012.01.007">10.1016/j.gde.2012.01.007</a>.
  short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012)
    132–138.
date_created: 2021-06-08T08:58:52Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-12-14T08:32:38Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2012.01.007
extern: '1'
external_id:
  pmid:
  - '22336527'
intvolume: '        22'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 132-138
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of biological accuracy, precision, and memory by plant chromatin
  organization
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 22
year: '2012'
...
---
OA_type: closed access
_id: '4198'
abstract:
- lang: eng
  text: Animal body plan arises during gastrulation and organogenesis by the coordination
    of inductive events and cell movements. Several signaling pathways, such as BMP,
    FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate
    specification during vertebrate embryogenesis. Growing evidence indicates that
    BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so
    through mechanisms distinct from those that specify cell fates. Moreover, pathways
    controlling cell movements can also indirectly influence cell fate specification
    by regulating dimensions and relative positions of interacting tissues. The current
    challenge is to delineate the molecular mechanisms via which the major signaling
    pathways regulate cell fate specification and movements, and how these two processes
    are coordinated to ensure normal development.
article_processing_charge: No
article_type: review
author:
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
- first_name: Lilianna
  full_name: Solnica Krezel, Lilianna
  last_name: Solnica Krezel
citation:
  ama: Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification
    and movement during vertebrate gastrulation. <i>Current Opinion in Genetics &#38;
    Development</i>. 2008;18(4):311-316. doi:<a href="https://doi.org/10.1016/j.gde.2008.07.011">10.1016/j.gde.2008.07.011</a>
  apa: Heisenberg, C.-P. J., &#38; Solnica Krezel, L. (2008). Back and forth between
    cell fate specification and movement during vertebrate gastrulation. <i>Current
    Opinion in Genetics &#38; Development</i>. Elsevier. <a href="https://doi.org/10.1016/j.gde.2008.07.011">https://doi.org/10.1016/j.gde.2008.07.011</a>
  chicago: Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth
    between Cell Fate Specification and Movement during Vertebrate Gastrulation.”
    <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2008. <a href="https://doi.org/10.1016/j.gde.2008.07.011">https://doi.org/10.1016/j.gde.2008.07.011</a>.
  ieee: C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate
    specification and movement during vertebrate gastrulation,” <i>Current Opinion
    in Genetics &#38; Development</i>, vol. 18, no. 4. Elsevier, pp. 311–316, 2008.
  ista: Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate
    specification and movement during vertebrate gastrulation. Current Opinion in
    Genetics &#38; Development. 18(4), 311–316.
  mla: Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between
    Cell Fate Specification and Movement during Vertebrate Gastrulation.” <i>Current
    Opinion in Genetics &#38; Development</i>, vol. 18, no. 4, Elsevier, 2008, pp.
    311–16, doi:<a href="https://doi.org/10.1016/j.gde.2008.07.011">10.1016/j.gde.2008.07.011</a>.
  short: C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics &#38;
    Development 18 (2008) 311–316.
date_created: 2018-12-11T12:07:32Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2026-05-28T14:03:47Z
day: '01'
doi: 10.1016/j.gde.2008.07.011
extern: '1'
external_id:
  pmid:
  - '18721878'
intvolume: '        18'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 311 - 316
pmid: 1
publication: Current Opinion in Genetics & Development
publication_identifier:
  eissn:
  - 1879-0380
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
publist_id: '1918'
status: public
title: Back and forth between cell fate specification and movement during vertebrate
  gastrulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 18
year: '2008'
...
---
_id: '9529'
abstract:
- lang: eng
  text: Eukaryotic organisms have the remarkable ability to inherit states of gene
    activity without altering the underlying DNA sequence. This epigenetic inheritance
    can persist over thousands of years, providing an alternative to genetic mutations
    as a substrate for natural selection. Epigenetic inheritance might be propagated
    by differences in DNA methylation, post-translational histone modifications, and
    deposition of histone variants. Mounting evidence also indicates that small interfering
    RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining
    states of gene activity. Much of the epigenetic machinery of many organisms, including
    Arabidopsis, appears to be directed at silencing viruses and transposable elements,
    with epigenetic regulation of endogenous genes being mostly derived from such
    processes.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: 'Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective
    silence. <i>Current Opinion in Genetics and Development</i>. 2005;15(5):557-562.
    doi:<a href="https://doi.org/10.1016/j.gde.2005.07.002">10.1016/j.gde.2005.07.002</a>'
  apa: 'Zilberman, D., &#38; Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis:
    Selective silence. <i>Current Opinion in Genetics and Development</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.gde.2005.07.002">https://doi.org/10.1016/j.gde.2005.07.002</a>'
  chicago: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
    Selective Silence.” <i>Current Opinion in Genetics and Development</i>. Elsevier,
    2005. <a href="https://doi.org/10.1016/j.gde.2005.07.002">https://doi.org/10.1016/j.gde.2005.07.002</a>.'
  ieee: 'D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective
    silence,” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5.
    Elsevier, pp. 557–562, 2005.'
  ista: 'Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective
    silence. Current Opinion in Genetics and Development. 15(5), 557–562.'
  mla: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
    Selective Silence.” <i>Current Opinion in Genetics and Development</i>, vol. 15,
    no. 5, Elsevier, 2005, pp. 557–62, doi:<a href="https://doi.org/10.1016/j.gde.2005.07.002">10.1016/j.gde.2005.07.002</a>.'
  short: D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15
    (2005) 557–562.
date_created: 2021-06-08T09:05:56Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-12-14T09:13:13Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2005.07.002
extern: '1'
external_id:
  pmid:
  - '16085410'
intvolume: '        15'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 557-562
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Epigenetic inheritance in Arabidopsis: Selective silence'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2005'
...