Evidence map›Paper›PMID 38251974›Full record

ArticleeLife2024

Regulation of nuclear transcription by mitochondrial RNA in endothelial cells.

Kiran Sriram, Zhijie Qi, Dongqiang Yuan, Naseeb Kaur Malhi, Xuejing Liu, Riccardo Calandrelli, Yingjun Luo, Alonso Tapia, Shengyan Jin, Ji Shi and 9 more

Open access · goldAbstract read
In one paragraph

Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
2.3field-weighted citation impact, top 11% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

16 citing papers in PubMed, 15 citations in OpenAlex.

  1. Trial
  2. Review
  3. Review
  4. Review
  5. Article
  6. Review
  7. Article
  8. Review
  9. Mitochondria - the CEO of the cell.Journal of cell science · 2025
    Review
  10. Article
  11. Mitochondrial RNA in Inflammation.International journal of biological sciences · 2025
    Review
  12. Mitochondrial epigenetic mechanisms in cancer: an updated overview.Frontiers in cell and developmental biology · 2025
    Review
  13. Review
  14. Review
  15. Article
  16. Spatial detection of mitochondrial DNA and RNA in tissues.Frontiers in cell and developmental biology · 2024
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors at 4 institutions in 1 country.

Kiran SriramDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.ORCID https://orcid.org/0000-0002-7412-2380
Zhijie QiDepartment of Bioengineering, University of California San Diego, La Jolla, United States.ORCID https://orcid.org/0000-0002-0022-8844
Dongqiang YuanDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.
Naseeb Kaur MalhiDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.ORCID https://orcid.org/0000-0002-8981-2974
Xuejing LiuDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.ORCID https://orcid.org/0000-0002-3931-0191
Riccardo CalandrelliDepartment of Bioengineering, University of California San Diego, La Jolla, United States.ORCID https://orcid.org/0000-0002-4541-6320
Yingjun LuoDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.
Alonso TapiaDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.
Shengyan JinDepartment of Genetics, Yale University School of Medicine, New Haven, United States.ORCID https://orcid.org/0000-0002-8667-7586
Ji ShiTranslura, Inc, New Haven, United States.
Martha SalasDepartment of Stem Cell Biology and Regenerative Medicine, City of Hope, Duarte, United States.ORCID https://orcid.org/0009-0006-0159-5896
Runrui DangDepartment of Bioengineering, University of California Riverside, Riverside, United States.
Brian ArmstrongDepartment of Stem Cell Biology and Regenerative Medicine, City of Hope, Duarte, United States.ORCID https://orcid.org/0009-0003-5026-2631
Saul J PricemanDepartment of Hematology & Hematopoietic Cell Transplantation, Department of Immuno-oncology, City of Hope, Duarte, United States.ORCID https://orcid.org/0000-0002-8136-2112
Ping H WangDepartment of Diabetes, Endocrinology, and Metabolism, City of Hope, Duarte, United States.ORCID https://orcid.org/0000-0002-7847-7752
Jiayu LiaoDepartment of Bioengineering, University of California Riverside, Riverside, United States.
Rama NatarajanDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.ORCID https://orcid.org/0000-0003-4494-1788
Sheng ZhongDepartment of Bioengineering, University of California San Diego, La Jolla, United States.
Zhen Bouman ChenDepartment of Diabetes Complications and Metabolism, City of Hope, Duarte, United States.ORCID https://orcid.org/0000-0002-3291-1090
City of Hope · USUniversity of California San Diego · USUniversity of California, Riverside · USYale University · US

Funding

Transgenic Mouse FacilityP30CA033572 · NCI · CITY OF HOPE/BECKMAN RESEARCH INSTITUTE · PI XIWEI WU · 1985 to 2026
$86.3M
Transcriptional Regulation by Angiotensin II in Vascular Smooth Muscle CellsR01HL106089 · NHLBI · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI NATARAJAN, RAMA · 2011 to 2024
$6.6M
Transforming growth factor beta1, microRNAs, lncRNA and diabetic nephropathyR01DK081705 · NIDDK · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI NATARAJAN, RAMA · 2009 to 2023
$6.1M
Extremely high-throughput mapping of protein, RNA, and chromatin interactions in health and diseaseDP1DK126138 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHONG, SHENG · 2020 to 2024
$3.7M
Single Cell Tracking of 3D Epigenetic Landscape Evolution During Embryonic DevelopmentR01HD107206 · NICHD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Yingxiao Wang, Sheng Zhong · 2022 to 2026
$3.2M
Long non-coding RNA-mediated chromatin remodeling in angiogenesisR01HL145170 · NHLBI · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI CHEN, ZHEN BOUMAN · 2019 to 2023
$2.6M
RNA-mediated endotheliopathy in diabetic vasculopathyR35HL171550 · NHLBI · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI Zhen Bouman Chen · 2024 to 2026
$2.2M
Revealing protein-protein interactions and RNA-protein interactions at genome-scale in two weeksR01GM138852 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHONG, SHENG · 2020 to 2023
$1.5M
NCI NIH HHS P30 CA033572NHLBI NIH HHS R01 HL106089NHLBI NIH HHS R01 HL145170NHLBI NIH HHS R35 HL171550NICHD NIH HHS R01 HD107206NIDDK NIH HHS DP1 DK126138NIDDK NIH HHS R01 DK081705NIGMS NIH HHS R01 GM138852NIH HHS DP1DK126138NIH HHS P30CA033572NIH HHS R01GM138852NIH HHS R01HD107206NIH HHS R01HL106089NIH HHS R01HL145170
6 · The paper itself

Abstract

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, thus termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.

Indexed as

Endothelial CellsRNABiological AssayChromatinHumansRNA, MitochondrialChromatinRNARNA, Mitochondrialchromatinchromosomesdiabetesendothelial cellsgene expressionhumanimmunologyinflammationinnate immunitylncRNAmitochondrial RNAnucleustranscription

Identifiers

PMID38251974
PMCPMC10803041
OpenAlexW4391109770

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.