Research Description

Nuclear Export and Localization of mRNA

A human cell line showing the endoplasmic reticulum (yellow) and nucleus (blue).

Gene expression plays a critical role in regulating and modifying various cellular functions, which impact on processes such as development and homeostasis. Gene activation begins in the nucleus, where DNA is transcribed into an RNA nascent transcript that is processed so that non-coding introns are removed by the splicesome, and a cap and poly-A tail are added to the beginning and end of the RNA. Once processing is complete, the mature messenger RNA (mRNA) is exported to the cytoplasm where it localizes to distinct subcellular sites. For example in higher eukaryotes, mRNAs coding for secreted and membrane bound proteins are targeted to the surface of the endoplasmic reticulum (ER).

Our lab utilizes sophisticated cell manipulation protocols, such as nuclear microinjection, in order to figure out:

1) How are mRNAs exported from the nucleus?
2) How are mRNAs localized to their proper subcellular destination, such as the endoplasmic reticulum?
3) How does mRNA translation in the cytosol differ from translation on the endoplasmic reticulum?

We have found that certain human mRNAs require high GC-content for their efficient export from the nucleus. We have recently used computational biology to examine evolutionary forces that shape nucleotide content in human genes. In particular we wish to understand:

4) How do adaptive and non-adaptive evolutionary forces shape nucleotide content in human protein-coding genes?

Nuclear export of mRNA

We are currently trying to figure out how meaningful information is extracted from our genome, which is mostly comprised of junk DNA. A central player in cellular information processing is the mRNA nuclear export machinery.

Ftz mRNA transits through nuclear speckles (marked by SC35 and Aly) in preparation for nuclear export.

All RNA synthesis occurs in the nucleus. However, it is clear that only certain types of RNA are allowed to be exported to the cytoplasm. We are trying to define:

1) the rules that dictate whether any given mRNA is exported to the cytoplasm, retained in the nucleus or degraded

2) the underlying mechanisms that enforce these various fates.

Ribonucleoprotein complexes

All RNAs are packaged into larger ribonucleoprotein (RNP) complexes. These complexes may vary considerably between different types of mRNA. The protein component of the RNP dictates where the packaged mRNA is transported, how stable it is, and how efficiently it is translated into protein. We are trying to determine how and where these complexes are assembled and modified throughout the course of an mRNA’s lifetime.

Our work has indicated that messenger RNPs may be modified after they exit the nucleus through the nuclear pore. We have discovered that one nuclear pore protein, RanBP2/Nup358, directly interacts with mRNAs that encode for secretory proteins. Mutations in this gene have been associated with Acute Necrotizing Encephalopathy 1 (ANE1), a rare condition where cytokines are overproduced in response to viral infection. We are currently investigating whether ANE1-associated mutations alter how RanBP2 interacts with cytokine mRNAs.

Targeting of mRNAs to the endoplasmic reticulum

p180 (green) acts as an mRNA (red) receptor on the ER.

Secretory and membrane-bound proteins are synthesized from mRNAs that are localized to the surface of the endoplasmic reticulum (ER). We have discovered that the ER contains mRNA receptors that aid in this process. We hope to uncover:

1) the mechanism by which mRNA receptors facilitate ER-association of certain mRNAs

2) the elements within these mRNAs that determines their targeting to the ER

3) differences between the composition of cytoplasmic and ER-bound ribonucleoprotein complexes.

Differences between translation in the cytosol and on the endoplasmic reticulum

It has been long known that translation in the cytosol and on the surface of the endoplasmic reticulum differ, but the underlying reasons for this are mysterious. We have identified differences between the proteome of cytosolic and endoplasmic reticulum-associated polysomes by mass spectrometry. We are currently investigating how these differences influence mRNA translation in these two compartments.

Evolution of nucleotide content in genes

Nucleotide content averaged across exons (yellow) and introns (white) for all human protein-coding genes with exactly five exons.

It is generally assumed that the nucleotide content in genes is influenced solely by adaptive evolution, however we have found that certain patterns, such as the peak of GC-content at the start of human protein-coding genes is dictated by historical rates of recombination.

We are interesting in understanding all the forces that dictate nucleotide content. For the time being we are exploring this using phylogenitic analysis, comparative genomics, and in silico simulations of gene evolution. We aim to understand how these patterns are shaped by adaptive and non-adaptive forces.

Publications

View all publications on PubMed

RanBP2/Nup358 Mediates Sumoylation of STAT1 and Antagonizes Interferon-α-Mediated Antiviral Innate Immunity.
Li J, Su L, Jiang J, Wang YE, Ling Y, Qiu Y, Yu H, Wu J, Jiang S, Zhang T, Palazzo AF*, and Shen Q*
International Journal of Molecular Sciences, 2024, 25(1):299  Read

mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts.
Palazzo AF, Qiu Y, and Kang YM
RNA Biology. 2024, 21(1):1-12  Read

Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling.
Kejiou NS, Ilan L, Aigner S, Luo E, Tonn T, Ozadam H, Lee M, Cole GB, Rabano I, Rajakulendran N, Yee BA, Najafabadi HS, Moraes TF, Angers S, Yeo GW, Cenik C, Palazzo AF.
Nuc Acid Res., 2023, 51(21):6461-6478  Read

ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5′ splice site motifs within nuclear speckles
Lee, ES, Smith, HW, Wolf, EJ, Guvenek, A, Wang, YE, Emili, A, Tian, B and Palazzo, AF
RNA 2022, 28 (6):878-894  Read

Architecture of the cytoplasmic face of the nuclear pore
Bley, CJ, Nie, S, Mobbs, GW, Petrovic, S, Gres, AT, Liu, X, Mukherjee, S, Harvey, S, Huber, FM, Lin, DH, Brown, B, Tang, AW, Rundlet, EJ, Correia, AR, Chen, S, Regmi, SG, Stevens, TA, Jette, CA, Dasso, M, Patke, A, Palazzo, AF, Kossiakoff, AA, and Hoelz A
Science 2022, 376:eabm9129  Read

Not functional yet a difference maker: Junk DNA as a case study.
Havstad J, and Palazzo AF
Biology & Philosophy, 2022, 37:29  Read

RanBP2/Nup358 enhances miRNA activity by sumoylating Argonautes
Shen, Q, Wang , YE, Truong, M, Mahadevan, K, Wu, JJ, Zhang, H, Li, J, Smith, HW, Smibert, CA and Palazzo, AF
PLOS Genetics 2021, 17(2): e1009378  Read

A proximity-dependent biotinylation map of a human cell
Go CD, Knight JDR, Rajasekharan A, Rathod B, Hesketh GG, Abe KT, Youn JY, Samavarchi-Tehrani P, Zhang H, Zhu LY, Popiel E, Lambert JP, Coyaud É, Cheung SWT, Rajendran D, Wong CJ, Antonicka CJ, Pelletier L, Raught B, Palazzo AF, Shoubridge EA, Gingras AC.
Nature, 2021, 595(7865):120-124.  Read

GC-content biases in protein-coding genes act as an "mRNA identity" feature for nuclear export.
Palazzo AF, Kang YM
Bioessays 2021, 43:2000197  Read

Functional Long Non-coding RNAs Evolve from Junk Transcripts.
Palazzo AF, Koonin EV
Cell 2020, 183:1143-1155  Read

TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes.
Lee ES, Wolf EJ, Ihn SSJ, Smith HW, Emili A, Palazzo AF
Nucleic Acids Research 2020, 48(20):11645-11663  Read

MKRN2 Physically Interacts with GLE1 to Regulate mRNA Export and Zebrafish Retinal Development.
Wolf EJ, Miles A, Lee ES, Nabeel-Shah S, Greenblatt JF, Palazzo AF, Tropepe V, Emili A
Cell Reports 2020, 31(8):107693  Read

Getting clear about the F-word in genomics
Linquist S, Doolittle WF, Palazzo AF
PLoS Genetics 2020, 16(4):e1008702  Read

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs.
Palazzo AF, Lee ES
Front Genet. 2018; 9:440  Read

Single-Molecule Quantification of Translation-Dependent Association of mRNAs with the Endoplasmic Reticulum.
Voigt F, Zhang H, Cui XA, Triebold D, Liu AX, Eglinger J, Lee ES, Chao JA, Palazzo AF
Cell Reports 2017, 21(13):3740-3753  Read

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.
Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP
RNA 2017, 23(3):270-283  Read

mRNA localization as a rheostat to regulate subcellular gene expression.
Kejiou NS, Palazzo AF
Wiley Interdiscip Rev RNA. 2017 8(4)  Read