Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans

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Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans. / Nepal, Chirag; Taranta, Andrzej; Hadzhiev, Yavor; Pundhir, Sachin; Mydel, Piotr; Lenhard, Boris; Müller, Ferenc; Andersen, Jesper B.

In: iScience, Vol. 23, No. 4, UNSP 101008, 2020, p. 1-27.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Nepal, C, Taranta, A, Hadzhiev, Y, Pundhir, S, Mydel, P, Lenhard, B, Müller, F & Andersen, JB 2020, 'Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans', iScience, vol. 23, no. 4, UNSP 101008, pp. 1-27. https://doi.org/10.1016/j.isci.2020.101008

APA

Nepal, C., Taranta, A., Hadzhiev, Y., Pundhir, S., Mydel, P., Lenhard, B., Müller, F., & Andersen, J. B. (2020). Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans. iScience, 23(4), 1-27. [UNSP 101008]. https://doi.org/10.1016/j.isci.2020.101008

Vancouver

Nepal C, Taranta A, Hadzhiev Y, Pundhir S, Mydel P, Lenhard B et al. Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans. iScience. 2020;23(4):1-27. UNSP 101008. https://doi.org/10.1016/j.isci.2020.101008

Author

Nepal, Chirag ; Taranta, Andrzej ; Hadzhiev, Yavor ; Pundhir, Sachin ; Mydel, Piotr ; Lenhard, Boris ; Müller, Ferenc ; Andersen, Jesper B. / Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans. In: iScience. 2020 ; Vol. 23, No. 4. pp. 1-27.

Bibtex

@article{a00885b438644058a1f503f90981628f,

title = "Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans",

abstract = "HOTAIR was proposed to regulate either HoxD cluster genes in trans or HoxC cluster genes in cis, a mechanism that remains unclear. We have identified a 32-nucleotide conserved noncoding element (CNE) as HOTAIR ancient sequence that likely originated at the root of vertebrate. The second round of whole-genome duplication resulted in one copy of the CNE within HOTAIR and another copy embedded in noncoding transcript of HOXD11. Paralogous CNEs underwent compensatory mutations, exhibit sequence complementarity with respect to transcripts directionality, and have high affinity in vitro. The HOTAIR CNE resembled a poised enhancer in stem cells and an active enhancer in HOTAIR-expressing cells. HOTAIR expression is positively correlated with HOXC11 in cis and negatively correlated with HOXD11 in trans. We propose a dual modality of HOTAIR regulation where transcription of HOTAIR and its embedded enhancer regulates HOXC11 in cis and sequence complementarity between paralogous CNEs suggests HOXD11 regulation in trans.",

author = "Chirag Nepal and Andrzej Taranta and Yavor Hadzhiev and Sachin Pundhir and Piotr Mydel and Boris Lenhard and Ferenc M{\"u}ller and Andersen, {Jesper B}",

year = "2020",

doi = "10.1016/j.isci.2020.101008",

language = "English",

volume = "23",

pages = "1--27",

journal = "iScience",

issn = "2589-0042",

publisher = "Elsevier",

number = "4",

}

RIS

TY - JOUR

T1 - Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans

AU - Nepal, Chirag

AU - Taranta, Andrzej

AU - Hadzhiev, Yavor

AU - Pundhir, Sachin

AU - Mydel, Piotr

AU - Lenhard, Boris

AU - Müller, Ferenc

AU - Andersen, Jesper B

PY - 2020

Y1 - 2020

N2 - HOTAIR was proposed to regulate either HoxD cluster genes in trans or HoxC cluster genes in cis, a mechanism that remains unclear. We have identified a 32-nucleotide conserved noncoding element (CNE) as HOTAIR ancient sequence that likely originated at the root of vertebrate. The second round of whole-genome duplication resulted in one copy of the CNE within HOTAIR and another copy embedded in noncoding transcript of HOXD11. Paralogous CNEs underwent compensatory mutations, exhibit sequence complementarity with respect to transcripts directionality, and have high affinity in vitro. The HOTAIR CNE resembled a poised enhancer in stem cells and an active enhancer in HOTAIR-expressing cells. HOTAIR expression is positively correlated with HOXC11 in cis and negatively correlated with HOXD11 in trans. We propose a dual modality of HOTAIR regulation where transcription of HOTAIR and its embedded enhancer regulates HOXC11 in cis and sequence complementarity between paralogous CNEs suggests HOXD11 regulation in trans.

AB - HOTAIR was proposed to regulate either HoxD cluster genes in trans or HoxC cluster genes in cis, a mechanism that remains unclear. We have identified a 32-nucleotide conserved noncoding element (CNE) as HOTAIR ancient sequence that likely originated at the root of vertebrate. The second round of whole-genome duplication resulted in one copy of the CNE within HOTAIR and another copy embedded in noncoding transcript of HOXD11. Paralogous CNEs underwent compensatory mutations, exhibit sequence complementarity with respect to transcripts directionality, and have high affinity in vitro. The HOTAIR CNE resembled a poised enhancer in stem cells and an active enhancer in HOTAIR-expressing cells. HOTAIR expression is positively correlated with HOXC11 in cis and negatively correlated with HOXD11 in trans. We propose a dual modality of HOTAIR regulation where transcription of HOTAIR and its embedded enhancer regulates HOXC11 in cis and sequence complementarity between paralogous CNEs suggests HOXD11 regulation in trans.

U2 - 10.1016/j.isci.2020.101008

DO - 10.1016/j.isci.2020.101008

M3 - Journal article

C2 - 32268280

VL - 23

SP - 1

EP - 27

JO - iScience

JF - iScience

SN - 2589-0042

IS - 4

M1 - UNSP 101008

ER -

ID: 239954304

Faculty of Law