1 | Genome organization and chromatin in HIV‑1 integration 

Sites of HIV‑1 inte­gra­tion are essen­tial deter­mi­nants of viral fate. Where in the cel­lu­lar genome HIV‑1 inte­grates will define whether and how will the virus be silenced and whether or not could it be reac­ti­vat­ed. We are inter­est­ed in under­stand­ing where HIV‑1 inserts into the host genome, and how those inte­gra­tion sites are arranged in three-dimen­sion­al nuclear space — from recur­rent tar­get genes and super-enhancer clus­ters to CTCT and TAD bound­aries (Mari­ni et al Nature 2015, Lucic et a Nat Com­mun. 2019, Michielet­to et al Nat Com­mun. 2019, Rhein­berg­er et al. Cell Reports 2023). Using 3D immuno-DNA FISH togeth­er with genome-wide map­ping, we fol­low these rules in pri­ma­ry CD4+ T cells and in microglia, the long-lived reser­voir of the cen­tral ner­vous sys­tem We com­bine our genom­ic and bioin­for­mat­ic analy­sis with phys­i­cal mod­el­ling (in col­lab­o­ra­tion with Andrea Maria Chiariel­lo and Andrea Fontana) to under­stand how HIV‑1 selects it’s pre­ferred chro­matin environment.

2 | RNA:DNA hybrids and splicing

Our recent find­ings show that HIV‑1 prefers to inte­grate at genom­ic fea­tures rich in RNA:DNA hybrids (R‑loops) and near nuclear speck­les, the com­part­ments where splic­ing is orga­nized. We showed that the splic­ing heli­case Aquar­ius, part of the Intron Bind­ing Com­plex, resolves these R‑loops at sites of inte­gra­tion in speck­le-asso­ci­at­ed, H3K36me3-marked chro­matin engaged by LEDGF/p75 (Pen­zo et al. Nat Microb 2025; Müller et al. EMBO J 2025). These events link where the virus lands to how host and viral genes are spliced and expressed. We are par­tic­u­lar­ly inter­est­ed in how these genom­ic fea­tures and splic­ing fac­tors, also known also to be involved in DNA repair might con­tribute to the intact­ness of the provi­ral genome. At the same time, we are explor­ing the rel­e­vance of the new­ly described involve­ment of the RNA por­tion of chro­matin (R‑loops) for the func­tion of HIV‑1 inte­grase allosteric inhibitors (Pen­zo et al, in preparation).

3 | T‑cell metabolism, chromatin and latency 

The main obsta­cle to a func­tion­al HIV cure is the latent reser­voir of provirus estab­lished in mem­o­ry CD4+ T cells, which can­not be erad­i­cat­ed with cur­rent anti­retro­vi­ral treat­ment. Our work was the first to point to PML Nuclear Bod­ies as the nuclear archi­tec­tur­al shel­ter of latent HIV‑1 genomes (Lusic et al. Cell Host Microbe 2013, Lucic et al. Adv Sci­ence 2025). While dis­sect­ing the mol­e­c­u­lar mech­a­nisms that estab­lish and main­tain laten­cy, we found that the oxida­tive phos­pho­ry­la­tion path­way and cel­lu­lar oxida­tive stress play a cen­tral role in HIV‑1 tran­scrip­tion­al con­trol, cou­pled with the dis­rup­tion of PML Nuclear bod­ies dur­ing acute infec­tion, and their ref­or­ma­tion dur­ing laten­cy estab­lish­ment (Shy­taj, Lucic et al. EMBO J 2020). Con­comi­tant­ly, dur­ing laten­cy estab­lish­ment infect­ed cells also down­reg­u­late the gly­colyt­ic path­way (Shy­taj et al. EMBO Mol Med 2021), point­ing to the very intrigu­ing inter­play between cel­lu­lar metab­o­lism and chro­matin orga­ni­za­tion. Two projects are fol­low­ing these find­ings- in one, we char­ac­ter­ize cel­lu­lar metabo­lites and find a dys­reg­u­la­tion of the methio­n­ine path­way with con­se­quences for chro­matin and HIV‑1 reac­ti­va­tion (Gia­r­di­na and Lucic, in prepa­ra­tion); in the oth­er, we describe SUMOy­la­tion-depen­dent tran­scrip­tion­al reg­u­la­tion in HIV‑1 infect­ed CD4+ T Cell (Gia­r­di­na and Lucic, in preparation).

4 | Genome organization at the borders

A new strand of the lab’s work asks whether the nuclear periph­ery is a sin­gle envi­ron­ment or sev­er­al. We find that active, super-enhancer–marked genes — includ­ing HIV-1’s own tar­get genes — shift toward the periph­ery when CD4+ T cells are acti­vat­ed, appar­ent­ly toward nuclear pores rather than the repres­sive lamina.

By map­ping the genome asso­ci­at­ed with the bas­ket nucle­o­porin Nup153 and fol­low­ing indi­vid­ual gene alle­les as cells acti­vate (de Cas­tro et al. BioRX­IV 2024), we are test­ing whether a per­mis­sive, pore-orga­nized com­part­ment sits along­side the repres­sive lam­i­na — and whether pore num­ber itself helps set how the genome is arranged.

These ques­tions are part of a broad­er move toward the chro­matin biol­o­gy of pri­ma­ry human T cells at mol­e­c­u­lar res­o­lu­tion. Work­ing with the Beck and Hum­mer lab­o­ra­to­ries, we recent­ly used in-situ cryo-elec­tron tomog­ra­phy to resolve indi­vid­ual nucle­o­somes and map the archi­tec­ture of het­e­rochro­matin at the nuclear periph­ery of rest­ing T cells — a step toward read­ing genome orga­ni­za­tion direct­ly, struc­ture by struc­ture (Kreysing et al., Nature Com­muns 2026).

Com­plete pub­li­ca­tion list (PubMed)

2026  Kreysing JP, Cruz-León S, Betz J, et al., Lusic M, Hum­mer G, Beck M. Mol­e­c­u­lar archi­tec­ture of het­e­rochro­matin at the nuclear periph­ery of pri­ma­ry human cells. Nature Com­mu­ni­ca­tions 17.

2025  Pen­zo C, Ozel I, Kuz­man M, et al., Paris­si V, Lusic M. Aquar­ius heli­case facil­i­tates HIV‑1 inte­gra­tion into R‑loop–enriched genom­ic regions. Nature Micro­bi­ol­o­gy.

2024  de Cas­tro IJ, Schus­ter L, Pati­no Gomes C, et al., Saka S, Lusic M. Nucle­o­pore com­plex har­bors splic­ing machin­ery for effi­cient mRNA pro­cess­ing. bioRx­iv.

2023  Rhein­berg­er M, Cos­ta AL, Kamp­mann M, et al., Her­rmann C, Lusic M. Genom­ic pro­fil­ing of HIV‑1 inte­gra­tion in microglia links viral inte­gra­tion to topo­log­i­cal­ly asso­ci­at­ed domains. Cell Reports 42:112110.

2022 Shy­taj IL, Feres M, Lucic B, Gal­lu­ci L, et al., Lusic M. The The FDA-approved drug cobici­s­tat syn­er­gizes with remde­sivir to inhib­it SARS-CoV­‑2 repli­ca­tion in vit­ro and decreas­es viral titers and dis­ease pro­gres­sion in Syr­i­an ham­sters. mBio 2022 Apr 26:13(2).

2021  Zila V, Mar­giot­ta E, Tur­oňová B, et al., Lusic M, Kräus­slich HG, Beck M. Cone-shaped HIV‑1 cap­sids are trans­port­ed through intact nuclear pores. Cell 184.

2019  Lucic B, Chen H‑C, Kuz­man M, et al., Fil­ion GJ, Lusic M. Spa­tial­ly clus­tered loci with mul­ti­ple enhancers are fre­quent tar­gets of HIV‑1. Nature Com­mu­ni­ca­tions 10:4059.

2017  Lusic M, Sili­ciano RF. Nuclear land­scape of HIV‑1 infec­tion and inte­gra­tion. Nature Reviews Micro­bi­ol­o­gy 15:69–82.

2015  Mari­ni B, Kertész-Farkas A, Ali H, et al., Giac­ca M, Lusic M. Nuclear archi­tec­ture dic­tates HIV‑1 inte­gra­tion site selec­tion. Nature 521:227–231.

2013  Lusic M, Mari­ni B, Ali H, Lucic B, Luz­za­ti R, Giac­ca M. Prox­im­i­ty to PML nuclear bod­ies neg­a­tive­ly reg­u­lates HIV‑1 gene expres­sion in CD4+ T cells. Cell Host & Microbe 13:665–677.